Variant report

Variant	rs2254249
Chromosome Location	chr7:6680674-6680675
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:6679104-6684327	K562	blood:	n/a	n/a
2	POLR2A	chr7:6679710-6680698	K562	blood:	n/a	n/a
3	POLR2A	chr7:6680572-6683184	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6627001..6634994-chr7:6673643..6681623,15	MCF-7	breast:
2	chr7:6668305..6670110-chr7:6679585..6681865,2	MCF-7	breast:

Variant related genes	Relation type
ZNF316	TF binding region
ENSG00000232581	Chromatin interaction
ENSG00000146576	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2140905	0.85[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2140907	0.81[CHD][hapmap]
rs2243544	0.85[CEU][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2246217	0.81[EUR][1000 genomes]
rs2249765	0.87[EUR][1000 genomes]
rs2250356	0.85[CEU][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2253869	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254504	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2264783	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2462656	0.96[ASN][1000 genomes]
rs2462657	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2464873	0.85[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2464877	0.96[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62439667	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs940874	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9640029	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
4	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv830895	chr7:6514781-6722092	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv508444	chr7:6534110-6700527	Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1025220	chr7:6534278-6736802	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv538717	chr7:6534278-6736802	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv887431	chr7:6535517-6690240	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv515978	chr7:6535517-6698905	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
11	nsv887432	chr7:6535517-6713985	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv887434	chr7:6557135-6713985	Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	nsv606001	chr7:6563109-6683454	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv606002	chr7:6567114-6713985	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
15	nsv887435	chr7:6613604-6713985	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
16	nsv824002	chr7:6618087-6716961	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv824003	chr7:6620920-6721409	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv887436	chr7:6626922-6721661	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	esv1797143	chr7:6628177-6705439	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
20	nsv606003	chr7:6628242-6713985	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	nsv606004	chr7:6643664-6692573	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv887437	chr7:6645281-6704332	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv887438	chr7:6652740-6709600	ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	esv1820840	chr7:6656753-6698297	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	esv1821128	chr7:6656753-6698297	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	esv1824232	chr7:6656753-6706631	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
27	esv1841674	chr7:6656753-6706631	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
28	nsv464297	chr7:6656897-6698905	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
29	nsv606005	chr7:6656897-6698905	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
30	nsv606006	chr7:6659509-6721661	ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
31	nsv606007	chr7:6666501-6692407	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
32	esv1803673	chr7:6671496-6721661	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
33	esv1834684	chr7:6671496-6721661	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
34	esv1800946	chr7:6673956-6706631	Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
35	esv1813782	chr7:6673956-6706631	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
36	esv1818550	chr7:6673956-6706631	Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
37	esv1826832	chr7:6673956-6706631	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
38	esv1839832	chr7:6673956-6706631	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
39	esv1851662	chr7:6673956-6706631	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6678000-6691600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:6678200-6681000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:6678200-6681000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:6678200-6681000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:6678200-6681200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:6678200-6681600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:6678200-6681600	Weak transcription	Fetal Kidney	kidney
8	chr7:6678200-6682400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:6678200-6683200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:6678200-6683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:6678200-6683800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:6678200-6684200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:6678200-6685000	Strong transcription	NHEK	skin
14	chr7:6678200-6698200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:6678400-6681000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:6678400-6681000	Weak transcription	Aorta	Aorta
17	chr7:6678400-6681200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr7:6678400-6683000	Weak transcription	Small Intestine	intestine
19	chr7:6678400-6691600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:6678400-6691600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:6678600-6681200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:6678600-6681200	Weak transcription	Brain Angular Gyrus	brain
23	chr7:6678600-6681600	Weak transcription	HUVEC	blood vessel
24	chr7:6678600-6682800	Weak transcription	Stomach Mucosa	stomach
25	chr7:6678600-6687800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:6678600-6687800	Strong transcription	Fetal Intestine Large	intestine
27	chr7:6678600-6689600	Strong transcription	Fetal Intestine Small	intestine
28	chr7:6678800-6680800	Genic enhancers	Dnd41	blood
29	chr7:6678800-6681400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:6678800-6681400	Strong transcription	HSMM	muscle
31	chr7:6678800-6681600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr7:6678800-6682000	Weak transcription	Psoas Muscle	Psoas
33	chr7:6678800-6685600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:6678800-6688600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:6678800-6689600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:6678800-6691200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr7:6678800-6691400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr7:6679000-6681200	Weak transcription	Fetal Lung	lung
39	chr7:6679000-6681400	Strong transcription	Primary B cells from cord blood	blood
40	chr7:6679000-6681800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr7:6679000-6682800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr7:6679000-6684600	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr7:6679000-6684800	Strong transcription	A549	lung
44	chr7:6679000-6687800	Strong transcription	Fetal Stomach	stomach
45	chr7:6679000-6689200	Strong transcription	Thymus	Thymus
46	chr7:6679000-6689400	Strong transcription	Fetal Thymus	thymus
47	chr7:6679000-6689600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr7:6679000-6690000	Strong transcription	Fetal Brain Female	brain
49	chr7:6679000-6692200	Strong transcription	Primary T cells from cord blood	blood
50	chr7:6679000-6692600	Strong transcription	Primary B cells from peripheral blood	blood

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