Variant report

Variant	rs1007661
Chromosome Location	chr2:231062616-231062617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1129411	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427293	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427294	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894695	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3948464	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4973299	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749386	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756480	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007920	chr2:230775427-231065592	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription 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	15 gene(s)	inside rSNPs	diseases
4	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1007661	SP110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231028400-231067000	Strong transcription	Primary B cells from peripheral blood	blood
2	chr2:231035400-231077000	Weak transcription	HepG2	liver
3	chr2:231035800-231062800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:231036800-231071800	Weak transcription	NHEK	skin
5	chr2:231036800-231073600	Weak transcription	HMEC	breast
6	chr2:231038000-231069600	Weak transcription	NHLF	lung
7	chr2:231041400-231064600	Weak transcription	Osteobl	bone
8	chr2:231043000-231062800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:231044800-231062800	Weak transcription	Pancreas	Pancrea
10	chr2:231045200-231062800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:231046200-231062800	Weak transcription	Right Ventricle	heart
12	chr2:231046200-231069800	Weak transcription	HSMM	muscle
13	chr2:231047600-231062800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:231048000-231062800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:231048200-231062800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:231048200-231062800	Weak transcription	Colonic Mucosa	Colon
17	chr2:231048200-231062800	Weak transcription	Gastric	stomach
18	chr2:231048200-231062800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:231048200-231062800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:231048400-231062800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:231049200-231062800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:231049200-231062800	Weak transcription	Esophagus	oesophagus
23	chr2:231050200-231065000	Weak transcription	Brain Substantia Nigra	brain
24	chr2:231050600-231062800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:231058600-231064200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:231058800-231063000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:231059000-231062800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:231059000-231082800	Weak transcription	Stomach Mucosa	stomach
29	chr2:231059800-231062800	Weak transcription	Left Ventricle	heart
30	chr2:231059800-231062800	Weak transcription	Lung	lung
31	chr2:231060200-231062800	Weak transcription	Aorta	Aorta
32	chr2:231061000-231067000	Weak transcription	Brain Angular Gyrus	brain
33	chr2:231062200-231062800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:231062200-231081600	Strong transcription	Liver	Liver
35	chr2:231062400-231062800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:231062400-231066800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:231062400-231074000	Strong transcription	Primary T cells from cord blood	blood
38	chr2:231062400-231081600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:231062600-231063000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
40	chr2:231062600-231063000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
41	chr2:231062600-231063000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
42	chr2:231062600-231063000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:231062600-231063000	Strong transcription	Fetal Intestine Large	intestine
44	chr2:231062600-231063000	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr2:231062600-231063000	ZNF genes & repeats	Psoas Muscle	Psoas
46	chr2:231062600-231063200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:231062600-231063200	ZNF genes & repeats	Primary B cells from cord blood	blood
48	chr2:231062600-231063200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr2:231062600-231063200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
50	chr2:231062600-231063200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood

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