Variant report

Variant	rs707899
Chromosome Location	chr6:26129948-26129949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26017750..26036418-chr6:26116875..26130553,65	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124529	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000124610	Chromatin interaction
ENSG00000137259	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10484432	0.92[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs1090949	0.81[YRI][hapmap]
rs1150658	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs1150659	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs1150663	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205050	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1543680	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16891325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16891344	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1773284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1773285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199757	0.81[YRI][hapmap]
rs2032444	0.84[CHD][hapmap]
rs2229768	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs2858996	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6931542	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707889	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs707890	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs707891	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs707892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs707893	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs707894	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs707896	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806976	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807203	0.81[YRI][hapmap]
rs807211	0.81[YRI][hapmap]
rs807213	0.81[YRI][hapmap]
rs8384	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
8	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
9	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
10	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
11	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
12	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
13	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
14	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
15	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
16	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
17	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
18	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs707899	ZNF187	cis	parietal	SCAN
rs707899	ZNF391	cis	cerebellum	SCAN
rs707899	HIST1H2AI	cis	parietal	SCAN
rs707899	HIST1H3H	cis	parietal	SCAN
rs707899	HIST1H1C	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26124600-26134200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:26126400-26130000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
3	chr6:26127000-26131200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:26127000-26131200	Weak transcription	Lung	lung
5	chr6:26127000-26141600	Weak transcription	Gastric	stomach
6	chr6:26127200-26130000	Weak transcription	Small Intestine	intestine
7	chr6:26127200-26131200	Weak transcription	Esophagus	oesophagus
8	chr6:26127200-26139400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:26127200-26139600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:26127400-26131400	Weak transcription	HSMM	muscle
11	chr6:26127600-26138800	Weak transcription	Aorta	Aorta
12	chr6:26127600-26138800	Weak transcription	Ovary	ovary
13	chr6:26127800-26130000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:26127800-26130200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:26127800-26130600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:26127800-26130600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:26127800-26130800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:26127800-26131200	Weak transcription	Right Ventricle	heart
19	chr6:26127800-26131800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:26127800-26132200	Strong transcription	Fetal Muscle Leg	muscle
21	chr6:26127800-26132400	Weak transcription	Fetal Heart	heart
22	chr6:26127800-26134200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr6:26127800-26136200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:26127800-26138600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:26127800-26140200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr6:26127800-26141800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:26127800-26143000	Weak transcription	NH-A	brain
28	chr6:26128000-26130000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:26128000-26130400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:26128000-26130400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:26128000-26131200	Weak transcription	Stomach Mucosa	stomach
32	chr6:26128000-26131800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:26128000-26132200	Genic enhancers	Placenta	Placenta
34	chr6:26128000-26132400	Strong transcription	Fetal Stomach	stomach
35	chr6:26128000-26133400	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr6:26128000-26141000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:26128200-26130000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:26128200-26130000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:26128200-26130200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:26128200-26131600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr6:26128200-26140800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:26128400-26130400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:26128400-26130600	Strong transcription	HSMMtube	muscle
44	chr6:26128400-26130800	Strong transcription	Osteobl	bone
45	chr6:26128400-26131200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:26128400-26131200	Strong transcription	Left Ventricle	heart
47	chr6:26128400-26132200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr6:26128600-26130200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:26128600-26130400	Genic enhancers	Fetal Kidney	kidney
50	chr6:26128600-26131200	Weak transcription	Pancreas	Pancrea

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