Variant report

Variant	rs7756881
Chromosome Location	chr6:26389926-26389927
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	MAFK	chr6:26389771-26390160	HepG2	liver:	n/a	chr6:26389965-26389974 chr6:26389957-26389972 chr6:26389964-26389974
2	MAFK	chr6:26389777-26390154	HepG2	liver:	n/a	chr6:26389965-26389974 chr6:26389957-26389972 chr6:26389964-26389974
3	MAFK	chr6:26389669-26390157	IMR90	lung:	n/a	chr6:26389965-26389974 chr6:26389957-26389972 chr6:26389964-26389974
4	MAFK	chr6:26389816-26390099	H1-hESC	embryonic stem cell:	n/a	chr6:26389965-26389974 chr6:26389957-26389972 chr6:26389964-26389974
5	RCOR1	chr6:26389494-26390006	K562	blood:	n/a	n/a
6	MAFK	chr6:26389537-26390170	K562	blood:	n/a	chr6:26389965-26389974 chr6:26389957-26389972 chr6:26389964-26389974
7	MAFK	chr6:26389777-26390153	Hela-S3	cervix:	n/a	chr6:26389965-26389974 chr6:26389957-26389972 chr6:26389964-26389974
8	CTCF	chr6:26389780-26389930	NHDF-neo	bronchial:	n/a	n/a
9	POLR2A	chr6:26389601-26389946	K562	blood:	n/a	n/a
10	YY1	chr6:26389842-26390005	K562	blood:	n/a	n/a
11	TEAD4	chr6:26389420-26390049	K562	blood:	n/a	n/a
12	ELF1	chr6:26389420-26389946	K562	blood:	n/a	chr6:26389708-26389721
13	MAFF	chr6:26389654-26390156	K562	blood:	n/a	chr6:26389955-26389973
14	MAX	chr6:26389435-26390052	K562	blood:	n/a	n/a
15	CEBPB	chr6:26389383-26389976	K562	blood:	n/a	n/a
16	MAFF	chr6:26389758-26390154	HepG2	liver:	n/a	chr6:26389955-26389973
17	ATF3	chr6:26389548-26389958	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26384661..26390027-chr6:26390440..26394308,9	K562	blood:
2	chr6:26378930..26384775-chr6:26385231..26390850,8	MCF-7	breast:
3	chr6:26283237..26286235-chr6:26387862..26389996,2	K562	blood:

Variant related genes	Relation type
BTN2A2	TF binding region
ENSG00000124508	Chromatin interaction
ENSG00000158406	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12189870	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12208220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757140	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3757142	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3757144	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3757145	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3757146	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3757148	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757149	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4490658	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912853	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs7757048	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775720	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461246	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs9461249	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9461250	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467728	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467729	0.93[ASN][1000 genomes]
rs9467730	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467731	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467732	0.80[AMR][1000 genomes]
rs9467733	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467734	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467735	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467736	0.84[AMR][1000 genomes]
rs9467738	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467739	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467740	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467741	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9467742	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467743	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467746	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467747	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv883491	chr6:26367689-26410800	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv883492	chr6:26367689-26436592	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv883493	chr6:26367689-26442786	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv883494	chr6:26367833-26442786	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv883495	chr6:26367833-26443853	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3334611	chr6:26367893-26443308	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
13	nsv883496	chr6:26369549-26413088	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv883497	chr6:26369549-26442786	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv883498	chr6:26369549-26443853	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv1030863	chr6:26371006-26405990	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv883499	chr6:26377591-26454454	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
18	esv3427999	chr6:26378373-26453532	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv462664	chr6:26379537-26451553	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv601184	chr6:26379537-26451553	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7756881	SCGN	cis	cerebellum	SCAN
rs7756881	BTN3A3	cis	cerebellum	SCAN
rs7756881	ZNF192	cis	parietal	SCAN
rs7756881	BTN3A1	cis	cerebellum	SCAN
rs7756881	BTN3A2	cis	parietal	SCAN
rs7756881	BTN3A2	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26384200-26390000	Weak transcription	Esophagus	oesophagus
2	chr6:26384200-26390000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:26384200-26390200	Weak transcription	Right Ventricle	heart
4	chr6:26384200-26390400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:26384200-26390600	Weak transcription	Gastric	stomach
6	chr6:26384200-26392200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:26384200-26393000	Weak transcription	Fetal Brain Female	brain
8	chr6:26384200-26393200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:26384200-26394600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:26384200-26394600	Weak transcription	Right Atrium	heart
11	chr6:26384200-26400800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:26384200-26400800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:26384200-26401000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:26384200-26401400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:26384200-26402000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:26384200-26402400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:26384200-26402400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:26384200-26402400	Weak transcription	Pancreas	Pancrea
19	chr6:26384400-26390200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:26384400-26390600	Weak transcription	Thymus	Thymus
21	chr6:26384400-26394200	Weak transcription	HUVEC	blood vessel
22	chr6:26384400-26401400	Weak transcription	Brain Angular Gyrus	brain
23	chr6:26384400-26402000	Weak transcription	Fetal Kidney	kidney
24	chr6:26384600-26390400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:26384600-26390800	Weak transcription	Left Ventricle	heart
26	chr6:26384600-26394400	Weak transcription	Fetal Intestine Large	intestine
27	chr6:26384600-26394400	Weak transcription	NHDF-Ad	bronchial
28	chr6:26384600-26394600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:26384600-26400800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:26384600-26401800	Weak transcription	Fetal Lung	lung
31	chr6:26384800-26390200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:26385000-26390200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:26385000-26390600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:26385200-26390200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:26385200-26390200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:26385200-26390400	Weak transcription	Fetal Thymus	thymus
37	chr6:26385200-26394600	Weak transcription	Brain Germinal Matrix	brain
38	chr6:26385200-26401000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:26385200-26401400	Weak transcription	Brain Substantia Nigra	brain
40	chr6:26385200-26401800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:26385400-26390600	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:26385400-26400800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:26385600-26390000	Weak transcription	Liver	Liver
44	chr6:26385800-26402000	Weak transcription	Colonic Mucosa	Colon
45	chr6:26386800-26392200	Strong transcription	Primary B cells from cord blood	blood
46	chr6:26387000-26390000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:26387000-26390600	Weak transcription	Aorta	Aorta
48	chr6:26387000-26394600	Weak transcription	Small Intestine	intestine
49	chr6:26387600-26390200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr6:26387800-26393400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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