Variant report

Variant	rs10885596
Chromosome Location	chr10:116444356-116444357
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	JUN	chr10:116444070-116445041	HUVEC	blood vessel:	n/a	chr10:116444820-116444833
2	NR3C1	chr10:116444224-116444513	A549	lung:	n/a	n/a
3	POLR2A	chr10:116443940-116444965	HUVEC	blood vessel:	n/a	n/a
4	KAP1	chr10:116444180-116445032	HEK293	kidney:	n/a	n/a
5	REST	chr10:116444107-116444382	SK-N-SH	brain:	n/a	n/a
6	TCF7L2	chr10:116444107-116444528	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr10:116443790-116445121	HUVEC	blood vessel:	n/a	n/a
8	JUND	chr10:116443698-116446290	SK-N-SH	brain:	n/a	chr10:116445995-116446006
9	EP300	chr10:116444108-116445088	A549	lung:	n/a	n/a
10	POLR2A	chr10:116444261-116444398	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr10:116444123-116444975	MCF10A-Er-Src	breast:	n/a	chr10:116444437-116444448 chr10:116444433-116444453 chr10:116444439-116444447
12	STAT3	chr10:116444032-116445002	MCF10A-Er-Src	breast:	n/a	chr10:116444437-116444448 chr10:116444433-116444453 chr10:116444439-116444447
13	BCL3	chr10:116444186-116445035	A549	lung:	n/a	n/a
14	STAT3	chr10:116443970-116445012	MCF10A-Er-Src	breast:	n/a	chr10:116444437-116444448 chr10:116444433-116444453 chr10:116444439-116444447
15	RCOR1	chr10:116444135-116444924	Hela-S3	cervix:	n/a	n/a
16	FOSL2	chr10:116444326-116445105	A549	lung:	n/a	n/a
17	MYC	chr10:116444099-116444363	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr10:116444120-116445060	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr10:116444068-116444995	MCF10A-Er-Src	breast:	n/a	n/a
20	MAX	chr10:116443889-116444512	A549	lung:	n/a	n/a
21	POLR2A	chr10:116444237-116445007	SK-N-SH	brain:	n/a	n/a
22	TEAD4	chr10:116444326-116445064	HepG2	liver:	n/a	n/a
23	GATA3	chr10:116444104-116445748	SK-N-SH	brain:	n/a	n/a
24	CEBPB	chr10:116444122-116444933	Hela-S3	cervix:	n/a	chr10:116444528-116444539
25	EP300	chr10:116444212-116445160	A549	lung:	n/a	n/a
26	ARID3A	chr10:116444339-116445521	HepG2	liver:	n/a	n/a
27	POLR2A	chr10:116444031-116444494	HUVEC	blood vessel:	n/a	n/a
28	GATA3	chr10:116444303-116444608	T-47D	breast:	n/a	n/a
29	POLR2A	chr10:116444037-116444542	HUVEC	blood vessel:	n/a	n/a
30	CEBPB	chr10:116444251-116444881	HepG2	liver:	n/a	chr10:116444528-116444539
31	GATA3	chr10:116444054-116445114	A549	lung:	n/a	n/a
32	TCF12	chr10:116443710-116445170	A549	lung:	n/a	n/a
33	SMC3	chr10:116444350-116444856	HepG2	liver:	n/a	n/a
34	POLR2A	chr10:116444101-116444957	HepG2	liver:	n/a	n/a
35	MYC	chr10:116443930-116444925	MCF10A-Er-Src	breast:	n/a	n/a
36	TCF12	chr10:116443949-116446182	SK-N-SH	brain:	n/a	chr10:116445841-116445851
37	TCF12	chr10:116443846-116446152	SK-N-SH	brain:	n/a	chr10:116445841-116445851
38	GATA2	chr10:116444164-116444985	HUVEC	blood vessel:	n/a	n/a
39	STAT3	chr10:116444096-116445005	MCF10A-Er-Src	breast:	n/a	chr10:116444437-116444448 chr10:116444433-116444453 chr10:116444439-116444447
40	FOS	chr10:116444036-116445084	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr10:116442825-116445041	PANC-1	pancreas:	n/a	n/a
42	SMC3	chr10:116444130-116444938	Hela-S3	cervix:	n/a	n/a
43	BHLHE40	chr10:116443983-116444431	HepG2	liver:	n/a	n/a
44	POLR2A	chr10:116443972-116444994	HUVEC	blood vessel:	n/a	n/a
45	EP300	chr10:116444328-116444917	HepG2	liver:	n/a	n/a
46	CREB1	chr10:116444060-116444484	A549	lung:	n/a	n/a
47	MAFK	chr10:116443836-116444414	HepG2	liver:	n/a	chr10:116444015-116444026 chr10:116444015-116444030 chr10:116444016-116444027 chr10:116444014-116444028 chr10:116444015-116444031 chr10:116444015-116444026 chr10:116444016-116444036
48	EP300	chr10:116444335-116444946	Hela-S3	cervix:	n/a	n/a
49	MAZ	chr10:116444311-116444634	HepG2	liver:	n/a	n/a
50	MAX	chr10:116444290-116444490	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:116444356-116444406	SK-N-SH_RA	brain:	n/a
2	chr10:116444356-116444406	Jurkat	blood:	n/a
3	chr10:116444356-116444406	IMR90	lung:	fetal
4	chr10:116444356-116444406	BJ	skin:	n/a
5	chr10:116444356-116444406	AG09319	gingival:	n/a
6	chr10:116444356-116444406	ECC-1	luminal epithelium:	n/a
7	chr10:116444356-116444406	HRE	kidney:	n/a
8	chr10:116444356-116444406	ProgFib	skin:	n/a
9	chr10:116444356-116444406	NHBE	bronchial:	n/a
10	chr10:116444356-116444406	BE2_C	brain:	n/a
11	chr10:116444356-116444406	A549	lung:	n/a
12	chr10:116444356-116444406	HCPEpiC	choroid plexus:	n/a
13	chr10:116444356-116444406	Hela-S3	cervix:	n/a
14	chr10:116444356-116444406	HCF	heart:	n/a
15	chr10:116444356-116444406	GM12892	blood:	n/a
16	chr10:116444356-116444406	HIPEpiC	eye:	n/a
17	chr10:116444356-116444406	GM12891	blood:	n/a
18	chr10:116444356-116444406	AoSMC	blood vessel:	n/a
19	chr10:116444356-116444406	HRCEpiC	kidney:	n/a
20	chr10:116444356-116444406	GM06990	blood:	n/a
21	chr10:116444356-116444406	AG04449	skin:	fetal
22	chr10:116444356-116444406	MCF-7	breast:	n/a
23	chr10:116444356-116444406	PFSK-1	brain:	n/a
24	chr10:116444356-116444406	GM12878	blood:	n/a
25	chr10:116444356-116444406	NHDF-neo	bronchial:	n/a
26	chr10:116444356-116444406	SK-N-MC	brain:	n/a
27	chr10:116444356-116444406	HCT-116	colon:	n/a
28	chr10:116444356-116444406	HAEpiC	amniotic membrane:	n/a
29	chr10:116444356-116444406	HNPCEpiC	eye:	n/a
30	chr10:116444356-116444406	NH-A	brain:	n/a
31	chr10:116444356-116444406	SAEC	small airway:	n/a
32	chr10:116444356-116444406	Caco-2	colon:	n/a
33	chr10:116444356-116444406	SKMC	muscle:	n/a
34	chr10:116444356-116444406	ovcar-3	ovarian:	n/a
35	chr10:116444356-116444406	K562	blood:	n/a
36	chr10:116444356-116444406	AG10803	skin:	n/a
37	chr10:116444356-116444406	HepG2	liver:	n/a
38	chr10:116444356-116444406	CMK	blood:	n/a
39	chr10:116444356-116444406	H1-hESC	embryonic stem cell:	embryo
40	chr10:116444356-116444406	HUVEC	blood vessel:	n/a
41	chr10:116444356-116444406	HL-60	blood:	n/a
42	chr10:116444356-116444406	HRPEpiC	eye:	n/a
43	chr10:116444356-116444406	NT2-D1	testis:	n/a
44	chr10:116444356-116444406	MCF10A-Er-Src	breast:	n/a
45	chr10:116444356-116444406	HEEpiC	esophagus:	n/a
46	chr10:116444356-116444406	HPAEpiC	pulmonary alveolar:	n/a
47	chr10:116444356-116444406	Hepatocyte	liver:	n/a
48	chr10:116444356-116444406	HMEC	breast:	n/a
49	chr10:116444356-116444406	PANC-1	pancreas:	n/a
50	chr10:116444356-116444406	AG04450	lung:	fetal

Variant related genes	Relation type
ABLIM1	TF binding region
ABLIM1	CpG island

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10885591	0.85[MKK][hapmap];1.00[AFR][1000 genomes]
rs10885592	0.85[MKK][hapmap];1.00[AFR][1000 genomes]
rs10885593	1.00[AFR][1000 genomes]
rs11196818	1.00[AFR][1000 genomes]
rs11196820	1.00[AFR][1000 genomes]
rs11196829	1.00[AFR][1000 genomes]
rs11196831	1.00[AFR][1000 genomes]
rs11196832	1.00[AFR][1000 genomes]
rs11196833	1.00[AFR][1000 genomes]
rs11196834	1.00[AFR][1000 genomes]
rs11196836	1.00[AFR][1000 genomes]
rs11196838	1.00[AFR][1000 genomes]
rs11196839	1.00[AFR][1000 genomes]
rs11196842	1.00[AFR][1000 genomes]
rs11196846	1.00[AFR][1000 genomes]
rs11196865	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11196867	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11196873	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11196876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196884	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11196905	1.00[CEU][hapmap];0.85[MEX][hapmap]
rs12161653	1.00[AFR][1000 genomes]
rs12572646	1.00[AFR][1000 genomes]
rs12573191	1.00[AFR][1000 genomes]
rs17092202	1.00[AFR][1000 genomes]
rs17092207	1.00[AFR][1000 genomes]
rs17092213	1.00[AFR][1000 genomes]
rs17092218	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[AFR][1000 genomes]
rs17092220	1.00[AFR][1000 genomes]
rs4447090	1.00[AFR][1000 genomes]
rs951268	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10885596	TCF7L2	cis	parietal	SCAN
rs10885596	PRDM8	trans	parietal	SCAN
rs10885596	KIAA1598	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116438600-116444800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr10:116439000-116444600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr10:116441200-116445200	Flanking Active TSS	HUVEC	blood vessel
4	chr10:116441400-116444400	Active TSS	Psoas Muscle	Psoas
5	chr10:116441400-116445600	Enhancers	Fetal Brain Male	brain
6	chr10:116441400-116446200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:116441600-116444600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr10:116441800-116445200	Weak transcription	Brain Angular Gyrus	brain
9	chr10:116441800-116445600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:116441800-116450800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr10:116442000-116444400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:116442000-116444400	Flanking Active TSS	Fetal Brain Female	brain
13	chr10:116442600-116445400	Flanking Active TSS	A549	lung
14	chr10:116442600-116445600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:116442800-116444600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr10:116443000-116444400	Weak transcription	Colon Smooth Muscle	Colon
17	chr10:116443000-116444600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:116443000-116445600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr10:116443200-116444400	Enhancers	Fetal Muscle Trunk	muscle
20	chr10:116443200-116444600	Flanking Active TSS	Fetal Intestine Large	intestine
21	chr10:116443200-116444600	Enhancers	Spleen	Spleen
22	chr10:116443200-116444600	Flanking Active TSS	HSMM	muscle
23	chr10:116443400-116444400	Active TSS	Brain Anterior Caudate	brain
24	chr10:116443400-116444400	Enhancers	Gastric	stomach
25	chr10:116443400-116444600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:116443400-116444600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:116443400-116444600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:116443400-116444600	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr10:116443400-116445200	Enhancers	Brain Germinal Matrix	brain
30	chr10:116443400-116445600	Enhancers	Placenta Amnion	Placenta Amnion
31	chr10:116443400-116446200	Enhancers	Small Intestine	intestine
32	chr10:116443600-116444400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr10:116443600-116444600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:116443600-116444600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:116443600-116444600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr10:116443600-116444600	Flanking Active TSS	NH-A	brain
37	chr10:116443600-116445400	Enhancers	Fetal Stomach	stomach
38	chr10:116443600-116445400	Flanking Active TSS	HepG2	liver
39	chr10:116443800-116444400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr10:116443800-116444600	Active TSS	Right Atrium	heart
41	chr10:116443800-116445200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:116443800-116445200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr10:116443800-116446000	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr10:116443800-116446000	Enhancers	Placenta	Placenta
45	chr10:116444000-116444400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr10:116444000-116444400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr10:116444000-116444400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr10:116444000-116444400	Enhancers	Fetal Heart	heart
49	chr10:116444000-116444400	Flanking Active TSS	Left Ventricle	heart
50	chr10:116444000-116444400	Enhancers	Ovary	ovary

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