Variant report

Variant	rs12375929
Chromosome Location	chr9:6902404-6902405
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	RCOR1	chr9:6902402-6902602	Hela-S3	cervix:	n/a	n/a
2	FOSL1	chr9:6902309-6902981	HCT-116	colon:	n/a	chr9:6902631-6902641 chr9:6902631-6902641 chr9:6902633-6902644 chr9:6902631-6902640 chr9:6902631-6902641 chr9:6902631-6902641
3	JUND	chr9:6902283-6902918	HCT-116	colon:	n/a	chr9:6902631-6902641 chr9:6902631-6902641 chr9:6902633-6902644 chr9:6902631-6902640 chr9:6902631-6902641 chr9:6902631-6902641
4	YY1	chr9:6902402-6902687	HCT-116	colon:	n/a	n/a
5	ATF2	chr9:6902404-6902842	GM12878	blood:	n/a	n/a
6	JUND	chr9:6902346-6902847	HCT-116	colon:	n/a	chr9:6902631-6902641 chr9:6902631-6902641 chr9:6902633-6902644 chr9:6902631-6902640 chr9:6902631-6902641 chr9:6902631-6902641
7	FOSL1	chr9:6902382-6902896	HCT-116	colon:	n/a	chr9:6902631-6902641 chr9:6902631-6902641 chr9:6902633-6902644 chr9:6902631-6902640 chr9:6902631-6902641 chr9:6902631-6902641

Variant related genes	Relation type
ENSG00000224972	TF binding region

Extended variants
information (count: 129 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

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];0.81[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10975861	0.85[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	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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]
rs10975883	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]
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	0.88[ASN][1000 genomes]
rs11789124	0.87[ASN][1000 genomes]
rs11789248	0.88[ASN][1000 genomes]
rs11789250	0.88[ASN][1000 genomes]
rs11790744	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11792447	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs11794598	0.88[ASN][1000 genomes]
rs11794707	0.92[CHB][hapmap];0.97[CHD][hapmap];0.88[ASN][1000 genomes]
rs11794732	0.88[ASN][1000 genomes]
rs12686353	0.80[CHD][hapmap]
rs1417293	0.86[EUR][1000 genomes]
rs1557004	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs17511187	0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[ASN][1000 genomes]
rs17511250	0.92[CHB][hapmap];0.97[CHD][hapmap]
rs17595667	0.92[CHB][hapmap];0.97[CHD][hapmap];0.88[ASN][1000 genomes]
rs17595843	0.88[ASN][1000 genomes]
rs17595877	0.92[CHB][hapmap];0.97[CHD][hapmap];0.88[ASN][1000 genomes]
rs17595898	0.88[ASN][1000 genomes]
rs17596052	0.80[CHD][hapmap]
rs35732562	0.83[CHD][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	0.88[ASN][1000 genomes]
rs56279813	0.88[ASN][1000 genomes]
rs56357252	0.88[ASN][1000 genomes]
rs57005961	0.90[ASN][1000 genomes]
rs57463825	0.96[ASN][1000 genomes]
rs58143962	0.88[ASN][1000 genomes]
rs58213169	0.88[ASN][1000 genomes]
rs58307562	0.88[ASN][1000 genomes]
rs58361204	0.88[ASN][1000 genomes]
rs58378352	0.88[ASN][1000 genomes]
rs58977474	0.88[ASN][1000 genomes]
rs59636651	0.88[ASN][1000 genomes]
rs59779500	0.97[ASN][1000 genomes]
rs59999598	0.88[ASN][1000 genomes]
rs60173310	0.86[ASN][1000 genomes]
rs61204407	0.87[ASN][1000 genomes]
rs62533762	0.88[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	0.87[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	0.90[ASN][1000 genomes]
rs62533827	0.90[ASN][1000 genomes]
rs62533828	0.90[ASN][1000 genomes]
rs62533829	0.90[ASN][1000 genomes]
rs62533830	0.90[ASN][1000 genomes]
rs62533831	0.90[ASN][1000 genomes]
rs62533832	0.90[ASN][1000 genomes]
rs62533833	0.90[ASN][1000 genomes]
rs62533834	0.90[ASN][1000 genomes]
rs6477122	0.82[CEU][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	0.88[ASN][1000 genomes]
rs68190370	0.88[ASN][1000 genomes]
rs7018886	0.82[GIH][hapmap];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[GIH][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[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	0.85[ASN][1000 genomes]
rs73405231	0.90[ASN][1000 genomes]
rs73410616	0.89[ASN][1000 genomes]
rs73639387	0.82[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];0.81[ASN][1000 genomes]
rs9792577	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
rs12375929	SLC1A1	cis	parietal	SCAN
rs12375929	KDM4C	cis	cerebellum	SCAN

Chromatin state (count:99 , 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	chr9:6875000-6902600	Weak transcription	HSMM	muscle
4	chr9:6880800-6907000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:6882800-6912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:6883000-6911800	Weak transcription	Psoas Muscle	Psoas
7	chr9:6887600-6902600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:6887600-6911800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:6888400-6902600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:6889600-6929000	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:6890000-6912000	Weak transcription	Spleen	Spleen
12	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
13	chr9:6890400-6911400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr9:6891800-6907000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:6893000-6909400	Strong transcription	Primary B cells from cord blood	blood
16	chr9:6893800-6908200	Weak transcription	Colonic Mucosa	Colon
17	chr9:6893800-6981600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr9:6894000-6921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:6894400-6906800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:6894800-6902600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:6894800-6902800	Weak transcription	Adipose Nuclei	Adipose
22	chr9:6894800-6911800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:6894800-6912000	Weak transcription	Fetal Muscle Leg	muscle
24	chr9:6894800-6922000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:6894800-6931600	Weak transcription	Dnd41	blood
26	chr9:6895200-6905400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:6895400-6902600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:6895600-6919800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:6896200-6959000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:6897000-6911800	Weak transcription	Pancreas	Pancrea
31	chr9:6897600-6932200	Weak transcription	Small Intestine	intestine
32	chr9:6898000-6902600	Weak transcription	Brain Angular Gyrus	brain
33	chr9:6898000-6902600	Weak transcription	Brain Substantia Nigra	brain
34	chr9:6898000-6905400	Weak transcription	Liver	Liver
35	chr9:6898200-6911800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr9:6898200-6911800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:6898200-6911800	Weak transcription	Stomach Mucosa	stomach
38	chr9:6898200-6921200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr9:6898200-6928800	Weak transcription	Ovary	ovary
40	chr9:6898200-6930800	Weak transcription	HSMMtube	muscle
41	chr9:6898400-6902600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:6898400-6912000	Weak transcription	Brain Anterior Caudate	brain
43	chr9:6899000-6905600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr9:6899400-6902800	Enhancers	Fetal Thymus	thymus
45	chr9:6900000-6906600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr9:6900000-6921200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr9:6900400-6905800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:6900600-6943000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr9:6900800-6902600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:6901600-6906200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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