Variant report

Variant	rs11771397
Chromosome Location	chr7:97878710-97878711
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	POLR2A	chr7:97878361-97878995	HUVEC	blood vessel:	n/a	n/a
2	SPI1	chr7:97878320-97878901	HL-60	blood:	n/a	chr7:97878612-97878621
3	GABPA	chr7:97878381-97878734	K562	blood:	n/a	n/a
4	POLR2A	chr7:97878231-97878878	HUVEC	blood vessel:	n/a	n/a
5	TAF1	chr7:97878401-97878782	PFSK-1	brain:	n/a	n/a
6	SPI1	chr7:97878427-97878804	HL-60	blood:	n/a	chr7:97878612-97878621
7	GABPA	chr7:97878444-97878800	A549	lung:	n/a	n/a
8	GABPA	chr7:97878369-97878872	K562	blood:	n/a	n/a
9	POLR2A	chr7:97878424-97878995	HUVEC	blood vessel:	n/a	n/a
10	GABPA	chr7:97878488-97878725	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr7:97878277-97879152	HUVEC	blood vessel:	n/a	n/a
12	GABPA	chr7:97878400-97878922	HL-60	blood:	n/a	n/a
13	GABPA	chr7:97878440-97878798	A549	lung:	n/a	n/a
14	POLR2A	chr7:97878335-97878816	PFSK-1	brain:	n/a	n/a
15	GABPA	chr7:97878267-97878946	HL-60	blood:	n/a	n/a
16	BRCA1	chr7:97878687-97878761	HepG2	liver:	n/a	n/a
17	GABPA	chr7:97878367-97878886	MCF-7	breast:	n/a	n/a
18	POLR2A	chr7:97878354-97878783	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
TECPR1	TF binding region
BRI3	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10249366	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10953247	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10953256	0.82[CHB][hapmap]
rs10953257	0.82[CHB][hapmap]
rs1132971	0.82[CHB][hapmap]
rs11761574	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11771953	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11772438	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11773779	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11984183	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12533016	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12539676	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12669622	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12704981	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12704983	0.82[CHB][hapmap]
rs12728	0.82[CHB][hapmap]
rs13232181	0.82[CHB][hapmap]
rs1468338	0.82[CHB][hapmap]
rs17436977	0.88[CHB][hapmap]
rs1859482	0.82[CHB][hapmap]
rs2107716	0.82[CHB][hapmap]
rs2270600	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2270604	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286074	0.82[CHB][hapmap]
rs2291747	0.85[CEU][hapmap]
rs2394827	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28566958	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28662014	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3801255	0.82[CHB][hapmap]
rs3801256	0.82[CHB][hapmap]
rs3801263	0.82[CHB][hapmap]
rs3801264	0.82[CHB][hapmap]
rs3823740	0.82[CHB][hapmap]
rs4727388	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4727390	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729421	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56098787	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61575270	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62479836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62479838	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6465664	0.81[CHB][hapmap]
rs6465666	0.82[CHB][hapmap]
rs6465667	0.82[CHB][hapmap]
rs6465672	0.82[CHB][hapmap]
rs6465675	0.82[CHB][hapmap]
rs6465680	0.80[CEU][hapmap]
rs6945554	0.82[CHB][hapmap]
rs6947340	0.82[CHB][hapmap]
rs6948540	0.82[CHB][hapmap]
rs6949718	0.81[CHB][hapmap]
rs6951479	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6955647	0.81[CHB][hapmap]
rs6961129	0.88[CHB][hapmap]
rs6963210	0.82[CHB][hapmap]
rs6968193	0.82[CHB][hapmap]
rs6970801	0.82[CHB][hapmap]
rs6970990	0.82[CHB][hapmap]
rs6975156	0.81[CHB][hapmap]
rs736753	0.82[CHB][hapmap]
rs7458551	0.82[CHB][hapmap]
rs747631	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs747632	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7776638	0.81[CHB][hapmap]
rs7777415	0.82[CHB][hapmap]
rs7781916	0.82[CHB][hapmap]
rs7787309	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7789380	0.82[CHB][hapmap]
rs7796762	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs7797943	0.82[CHB][hapmap]
rs7807455	0.82[CHB][hapmap]
rs7807555	0.82[CHB][hapmap]
rs954050	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1800947	chr7:97857675-97889672	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11771397	GATS	cis	cerebellum	SCAN
rs11771397	FIS1	cis	parietal	SCAN
rs11771397	TECPR1	cis	parietal	SCAN
rs11771397	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs11771397	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97841200-97880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:97841400-97879400	Weak transcription	Fetal Brain Male	brain
3	chr7:97841400-97880200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:97848000-97880600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:97853200-97880000	Weak transcription	A549	lung
6	chr7:97853400-97880200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:97857000-97879000	Strong transcription	Brain Germinal Matrix	brain
8	chr7:97858200-97879000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:97859200-97880200	Weak transcription	Psoas Muscle	Psoas
10	chr7:97864600-97880200	Weak transcription	NHDF-Ad	bronchial
11	chr7:97864600-97880200	Weak transcription	NHEK	skin
12	chr7:97865200-97880200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:97866000-97880400	Weak transcription	Fetal Kidney	kidney
14	chr7:97868200-97880200	Weak transcription	HSMM	muscle
15	chr7:97868600-97880000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:97868800-97880200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:97868800-97880200	Weak transcription	Colon Smooth Muscle	Colon
18	chr7:97869000-97880600	Weak transcription	NH-A	brain
19	chr7:97870400-97880000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:97870400-97880000	Weak transcription	Hela-S3	cervix
21	chr7:97870800-97880200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:97871200-97880000	Weak transcription	Fetal Lung	lung
23	chr7:97871400-97880000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:97871600-97879600	Weak transcription	Fetal Intestine Large	intestine
25	chr7:97871600-97880200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:97871800-97880400	Weak transcription	Osteobl	bone
27	chr7:97872800-97878800	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr7:97873800-97880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:97874000-97879800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:97874000-97880000	Weak transcription	Brain Angular Gyrus	brain
31	chr7:97874000-97880000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr7:97874000-97880200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:97874000-97880200	Weak transcription	HSMMtube	muscle
34	chr7:97874000-97880800	Weak transcription	Ovary	ovary
35	chr7:97874200-97879200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:97874200-97879800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:97874200-97880200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:97874200-97881000	Weak transcription	Aorta	Aorta
39	chr7:97874400-97880000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:97874400-97880200	Weak transcription	Brain Substantia Nigra	brain
41	chr7:97874400-97880200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr7:97874600-97878800	Weak transcription	Brain Anterior Caudate	brain
43	chr7:97874600-97880200	Weak transcription	Liver	Liver
44	chr7:97875000-97880000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr7:97875000-97880000	Weak transcription	Colonic Mucosa	Colon
46	chr7:97875400-97879600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:97875400-97880000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:97875400-97880200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr7:97875400-97880200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr7:97875600-97879200	Weak transcription	NHLF	lung

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