Variant report

Variant	rs12062882
Chromosome Location	chr1:85313108-85313109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10127852	0.84[YRI][hapmap]
rs11161466	0.81[MKK][hapmap]
rs11161467	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs12083676	0.90[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12088935	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55643822	1.00[EUR][1000 genomes]
rs55694361	1.00[EUR][1000 genomes]
rs55706573	1.00[EUR][1000 genomes]
rs55740600	1.00[EUR][1000 genomes]
rs55896911	1.00[EUR][1000 genomes]
rs56105173	1.00[EUR][1000 genomes]
rs72718711	1.00[EUR][1000 genomes]
rs72718712	1.00[EUR][1000 genomes]
rs72718713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72718714	1.00[EUR][1000 genomes]
rs72718717	1.00[EUR][1000 genomes]
rs72718718	1.00[EUR][1000 genomes]
rs72718722	1.00[EUR][1000 genomes]
rs72718724	1.00[EUR][1000 genomes]
rs72718725	1.00[EUR][1000 genomes]
rs72718726	1.00[EUR][1000 genomes]
rs72718727	1.00[EUR][1000 genomes]
rs72718728	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12062882	ZC3H7A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85289400-85330800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:85304000-85313200	Weak transcription	Gastric	stomach
3	chr1:85306200-85316000	Enhancers	Fetal Heart	heart
4	chr1:85309600-85313400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:85311400-85313800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:85311600-85313800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:85311600-85313800	Enhancers	Liver	Liver
8	chr1:85311600-85314600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:85311600-85317600	Enhancers	HMEC	breast
10	chr1:85311800-85313600	Enhancers	NHEK	skin
11	chr1:85311800-85313800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:85312000-85313600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:85312000-85313800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:85312000-85314200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:85312200-85313200	Enhancers	Osteobl	bone
16	chr1:85312200-85313800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:85312200-85313800	Enhancers	NHDF-Ad	bronchial
18	chr1:85312200-85314000	Enhancers	Fetal Lung	lung
19	chr1:85312200-85314000	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr1:85312200-85314200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:85312600-85313200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:85312600-85313600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:85312600-85313600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:85312600-85313600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:85312600-85313600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:85312600-85313600	Enhancers	Brain Hippocampus Middle	brain
27	chr1:85312600-85313600	Enhancers	HSMMtube	muscle
28	chr1:85312600-85313800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:85312600-85313800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr1:85312600-85313800	Enhancers	Hela-S3	cervix
31	chr1:85312600-85314000	Enhancers	Brain Cingulate Gyrus	brain
32	chr1:85312600-85314400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:85312600-85314400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:85312600-85314600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr1:85312800-85313200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr1:85312800-85313200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:85312800-85313200	Enhancers	Stomach Smooth Muscle	stomach
38	chr1:85312800-85313400	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:85312800-85313400	Enhancers	Fetal Intestine Small	intestine
40	chr1:85312800-85313400	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr1:85312800-85313600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:85312800-85313600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr1:85312800-85313600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:85312800-85313600	Enhancers	Brain Angular Gyrus	brain
45	chr1:85312800-85313600	Enhancers	Brain Anterior Caudate	brain
46	chr1:85312800-85313600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr1:85312800-85313800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr1:85312800-85313800	Enhancers	Brain Substantia Nigra	brain
49	chr1:85312800-85313800	Enhancers	NH-A	brain
50	chr1:85312800-85313800	Enhancers	NHLF	lung

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