Variant report

Variant	rs2254381
Chromosome Location	chr7:6679526-6679527
allele	C/T
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	chr7:6679480-6679554	K562	blood:	n/a	n/a
2	MAX	chr7:6679382-6679554	NB4	blood:	n/a	chr7:6679494-6679503 chr7:6679495-6679502
3	POLR2A	chr7:6679104-6684327	K562	blood:	n/a	n/a
4	CEBPB	chr7:6679421-6679645	A549	lung:	n/a	n/a
5	POLR2A	chr7:6679077-6679660	GM12878	blood:	n/a	n/a
6	CEBPB	chr7:6679441-6679533	K562	blood:	n/a	n/a
7	CEBPB	chr7:6679380-6679580	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6615800..6617832-chr7:6677563..6680150,2	MCF-7	breast:
2	chr7:6627001..6634994-chr7:6673643..6681623,15	MCF-7	breast:
3	chr7:6674043..6676883-chr7:6677067..6680291,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF853-2	chr7:6679361-6680635	ucscGeneNc_uc003sqr_1

Variant related genes	Relation type
ZNF316	TF binding region
ENSG00000146576	Chromatin interaction
ENSG00000136247	Chromatin interaction
ENSG00000232581	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1008000	0.81[AMR][1000 genomes]
rs2249393	0.81[AMR][1000 genomes]
rs2249754	0.81[AMR][1000 genomes]
rs2250243	0.81[AMR][1000 genomes]
rs2253738	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2253770	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254503	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2462660	0.81[AMR][1000 genomes]
rs2464876	0.81[AMR][1000 genomes]
rs940870	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6678000-6680600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:6678000-6691600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:6678200-6679600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr7:6678200-6679600	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr7:6678200-6679800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:6678200-6679800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:6678200-6679800	Genic enhancers	Fetal Muscle Leg	muscle
8	chr7:6678200-6680000	Enhancers	Fetal Heart	heart
9	chr7:6678200-6680000	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr7:6678200-6680400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:6678200-6680400	Weak transcription	NH-A	brain
12	chr7:6678200-6680600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:6678200-6680600	Weak transcription	HSMMtube	muscle
14	chr7:6678200-6681000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr7:6678200-6681000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:6678200-6681000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:6678200-6681200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr7:6678200-6681600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:6678200-6681600	Weak transcription	Fetal Kidney	kidney
20	chr7:6678200-6682400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:6678200-6683200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:6678200-6683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr7:6678200-6683800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:6678200-6684200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:6678200-6685000	Strong transcription	NHEK	skin
26	chr7:6678200-6698200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr7:6678400-6679600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:6678400-6679600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr7:6678400-6679800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:6678400-6679800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
31	chr7:6678400-6679800	Transcr. at gene 5' and 3'	K562	blood
32	chr7:6678400-6680000	Weak transcription	Right Atrium	heart
33	chr7:6678400-6680200	Weak transcription	Colonic Mucosa	Colon
34	chr7:6678400-6680400	Weak transcription	Ovary	ovary
35	chr7:6678400-6680400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr7:6678400-6681000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:6678400-6681000	Weak transcription	Aorta	Aorta
38	chr7:6678400-6681200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr7:6678400-6683000	Weak transcription	Small Intestine	intestine
40	chr7:6678400-6691600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:6678400-6691600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:6678600-6679600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr7:6678600-6679600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr7:6678600-6679600	Weak transcription	NHDF-Ad	bronchial
45	chr7:6678600-6679600	Weak transcription	Osteobl	bone
46	chr7:6678600-6679800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:6678600-6680000	Enhancers	Adipose Nuclei	Adipose
48	chr7:6678600-6680000	Weak transcription	Brain Substantia Nigra	brain
49	chr7:6678600-6680000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:6678600-6680400	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links