Variant report

Variant	rs10975883
Chromosome Location	chr9:6900898-6900899
allele	A/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	HNF4A	chr9:6900378-6900928	HepG2	liver:	n/a	chr9:6900879-6900893 chr9:6900879-6900894 chr9:6900880-6900892 chr9:6900879-6900894 chr9:6900879-6900894 chr9:6900435-6900443 chr9:6900879-6900892 chr9:6900746-6900761
2	HNF4G	chr9:6900449-6900939	HepG2	liver:	n/a	chr9:6900879-6900893 chr9:6900879-6900894 chr9:6900880-6900892 chr9:6900879-6900894 chr9:6900879-6900894 chr9:6900879-6900892
3	FOXA2	chr9:6900548-6901022	HepG2	liver:	n/a	n/a
4	HEY1	chr9:6900311-6900959	HepG2	liver:	n/a	n/a
5	TEAD4	chr9:6900213-6900961	HepG2	liver:	n/a	n/a
6	HNF4G	chr9:6900496-6900931	HepG2	liver:	n/a	chr9:6900879-6900893 chr9:6900879-6900894 chr9:6900880-6900892 chr9:6900879-6900894 chr9:6900879-6900894 chr9:6900879-6900892
7	MBD4	chr9:6900288-6900899	HepG2	liver:	n/a	n/a
8	SP1	chr9:6900324-6901033	HepG2	liver:	n/a	n/a
9	MYBL2	chr9:6900225-6900962	HepG2	liver:	n/a	n/a
10	HEY1	chr9:6900418-6900966	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:6900112-6900898	HepG2	liver:	n/a	n/a
12	TCF7L2	chr9:6900621-6900925	HepG2	liver:	n/a	n/a
13	ARID3A	chr9:6900480-6901015	HepG2	liver:	n/a	n/a
14	EP300	chr9:6900498-6900989	HepG2	liver:	n/a	chr9:6900968-6900982 chr9:6900703-6900712
15	RXRA	chr9:6900407-6901035	HepG2	liver:	n/a	chr9:6900879-6900892 chr9:6900878-6900894 chr9:6900879-6900892 chr9:6900876-6900896 chr9:6900879-6900892
16	HNF4A	chr9:6900447-6901027	HepG2	liver:	n/a	chr9:6900879-6900893 chr9:6900879-6900894 chr9:6900880-6900892 chr9:6900879-6900894 chr9:6900994-6901002 chr9:6900879-6900894 chr9:6900879-6900892 chr9:6900746-6900761
17	EP300	chr9:6900265-6901002	HepG2	liver:	n/a	chr9:6900968-6900982 chr9:6900703-6900712
18	POLR2A	chr9:6900317-6900927	HepG2	liver:	n/a	n/a
19	NFIC	chr9:6900427-6901163	HepG2	liver:	n/a	n/a
20	HDAC2	chr9:6900526-6900983	HepG2	liver:	n/a	chr9:6900968-6900982 chr9:6900969-6900983

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6896046..6898374-chr9:6899883..6901481,2	K562	blood:

Variant related genes	Relation type
ENSG00000224972	TF binding region

Extended variants
information (count: 127 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10465096	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10758808	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs10815472	0.80[TSI][hapmap]
rs10815473	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs10815474	0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815475	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs10815476	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10815477	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10815480	0.82[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10975861	0.82[CHD][hapmap]
rs10975871	1.00[CEU][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10975872	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs10975875	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10975878	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10975879	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10975888	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10975889	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11788152	0.88[ASN][1000 genomes]
rs11788187	0.88[ASN][1000 genomes]
rs11788687	0.88[ASN][1000 genomes]
rs11788849	0.87[ASN][1000 genomes]
rs11789124	0.87[ASN][1000 genomes]
rs11789248	0.87[ASN][1000 genomes]
rs11789250	0.87[ASN][1000 genomes]
rs11790744	0.92[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11792447	0.92[CHB][hapmap];0.87[ASN][1000 genomes]
rs11794598	0.87[ASN][1000 genomes]
rs11794707	0.92[CHB][hapmap];0.94[CHD][hapmap];0.87[ASN][1000 genomes]
rs11794732	0.87[ASN][1000 genomes]
rs12375929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1417293	0.86[EUR][1000 genomes]
rs1557004	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs17511187	0.92[CHB][hapmap];0.94[CHD][hapmap];0.89[ASN][1000 genomes]
rs17511250	0.92[CHB][hapmap];0.94[CHD][hapmap]
rs17595667	0.92[CHB][hapmap];0.94[CHD][hapmap];0.87[ASN][1000 genomes]
rs17595843	0.88[ASN][1000 genomes]
rs17595877	0.92[CHB][hapmap];0.94[CHD][hapmap];0.88[ASN][1000 genomes]
rs17595898	0.88[ASN][1000 genomes]
rs35732562	0.86[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs3802406	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs55686117	0.88[ASN][1000 genomes]
rs55790433	0.88[ASN][1000 genomes]
rs56036039	0.88[ASN][1000 genomes]
rs56185621	0.87[ASN][1000 genomes]
rs56279813	0.88[ASN][1000 genomes]
rs56357252	0.88[ASN][1000 genomes]
rs57005961	0.89[ASN][1000 genomes]
rs57463825	0.97[ASN][1000 genomes]
rs58143962	0.87[ASN][1000 genomes]
rs58213169	0.88[ASN][1000 genomes]
rs58307562	0.87[ASN][1000 genomes]
rs58361204	0.88[ASN][1000 genomes]
rs58378352	0.88[ASN][1000 genomes]
rs58977474	0.88[ASN][1000 genomes]
rs59636651	0.87[ASN][1000 genomes]
rs59779500	0.96[ASN][1000 genomes]
rs59999598	0.88[ASN][1000 genomes]
rs60173310	0.86[ASN][1000 genomes]
rs61204407	0.86[ASN][1000 genomes]
rs62533762	0.87[ASN][1000 genomes]
rs62533769	0.88[ASN][1000 genomes]
rs62533773	0.88[ASN][1000 genomes]
rs62533774	0.88[ASN][1000 genomes]
rs62533787	0.88[ASN][1000 genomes]
rs62533788	0.88[ASN][1000 genomes]
rs62533789	0.88[ASN][1000 genomes]
rs62533791	0.88[ASN][1000 genomes]
rs62533792	0.88[ASN][1000 genomes]
rs62533794	0.87[ASN][1000 genomes]
rs62533818	0.86[ASN][1000 genomes]
rs62533819	0.87[ASN][1000 genomes]
rs62533820	0.88[ASN][1000 genomes]
rs62533821	0.88[ASN][1000 genomes]
rs62533822	0.88[ASN][1000 genomes]
rs62533823	0.88[ASN][1000 genomes]
rs62533824	0.87[ASN][1000 genomes]
rs62533825	0.89[ASN][1000 genomes]
rs62533827	0.89[ASN][1000 genomes]
rs62533828	0.89[ASN][1000 genomes]
rs62533829	0.89[ASN][1000 genomes]
rs62533830	0.89[ASN][1000 genomes]
rs62533831	0.89[ASN][1000 genomes]
rs62533832	0.89[ASN][1000 genomes]
rs62533833	0.89[ASN][1000 genomes]
rs62533834	0.89[ASN][1000 genomes]
rs6477122	0.82[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6477123	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6477124	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6477125	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6477126	0.82[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs6477127	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67642242	0.89[ASN][1000 genomes]
rs67866005	0.87[ASN][1000 genomes]
rs68190370	0.88[ASN][1000 genomes]
rs7018886	0.83[TSI][hapmap]
rs7019977	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7021011	0.82[CEU][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7021241	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7033444	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7036701	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs7043713	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7048678	0.82[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs72701484	0.88[ASN][1000 genomes]
rs72701487	0.84[ASN][1000 genomes]
rs73405231	0.89[ASN][1000 genomes]
rs73410616	0.88[ASN][1000 genomes]
rs7850907	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs7866109	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs946926	1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9792577	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	esv2752309	chr9:6670448-6908200	Weak transcription Active TSS Enhancers Flanking Active TSS Genic 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	70 gene(s)	inside rSNPs	diseases
8	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
9	nsv870332	chr9:6694842-6911550	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv1016109	chr9:6712314-6924843	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv831499	chr9:6723287-6930933	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
13	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv831500	chr9:6847952-6992535	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv1801159	chr9:6865386-6901008	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10975883	KDM4C	cis	cerebellum	SCAN
rs10975883	SLC1A1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6869600-6909400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:6869800-6908000	Weak transcription	Fetal Stomach	stomach
3	chr9:6871000-6902200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:6874200-6902400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:6875000-6902600	Weak transcription	HSMM	muscle
6	chr9:6878200-6902400	Weak transcription	NHDF-Ad	bronchial
7	chr9:6879800-6902400	Weak transcription	Osteobl	bone
8	chr9:6880800-6907000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:6882800-6912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:6883000-6911800	Weak transcription	Psoas Muscle	Psoas
11	chr9:6887600-6902600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:6887600-6911800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:6888400-6902600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:6889600-6929000	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:6890000-6902400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:6890000-6902400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:6890000-6912000	Weak transcription	Spleen	Spleen
18	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
19	chr9:6890400-6911400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr9:6890600-6901400	Weak transcription	A549	lung
21	chr9:6890800-6902400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr9:6891600-6901200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:6891800-6902400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:6891800-6907000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:6893000-6909400	Strong transcription	Primary B cells from cord blood	blood
26	chr9:6893800-6908200	Weak transcription	Colonic Mucosa	Colon
27	chr9:6893800-6981600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr9:6894000-6902400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:6894000-6921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:6894400-6902400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr9:6894400-6906800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:6894800-6901400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:6894800-6902600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:6894800-6902800	Weak transcription	Adipose Nuclei	Adipose
35	chr9:6894800-6911800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:6894800-6912000	Weak transcription	Fetal Muscle Leg	muscle
37	chr9:6894800-6922000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr9:6894800-6931600	Weak transcription	Dnd41	blood
39	chr9:6895000-6902400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:6895200-6905400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:6895400-6901600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr9:6895400-6902400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:6895400-6902600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:6895600-6902400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr9:6895600-6902400	Weak transcription	Left Ventricle	heart
46	chr9:6895600-6902400	Weak transcription	Right Ventricle	heart
47	chr9:6895600-6902400	Weak transcription	GM12878-XiMat	blood
48	chr9:6895600-6919800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr9:6895800-6902400	Weak transcription	Lung	lung
50	chr9:6896200-6959000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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