Variant report

Variant	rs10082956
Chromosome Location	chr12:29504556-29504557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:29503193..29506083-chr12:30783016..30785826,2	MCF-7	breast:
2	chr12:29501467..29504234-chr12:29504488..29507414,2	K562	blood:
3	chr12:29501592..29504234-chr12:29504443..29507414,2	K562	blood:

Variant related genes	Relation type
ENSG00000087502	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10128781	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1035606	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1035607	0.86[EUR][1000 genomes]
rs10743657	0.82[AFR][1000 genomes]
rs10743658	0.82[AFR][1000 genomes]
rs10843390	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843391	0.95[CHB][hapmap];0.81[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843397	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10843398	0.82[AFR][1000 genomes]
rs10843403	0.83[AFR][1000 genomes]
rs11050203	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11050209	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1156242	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12831751	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278093	0.86[CHB][hapmap];0.86[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278094	0.81[AFR][1000 genomes]
rs3782513	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3815843	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4931178	0.82[AFR][1000 genomes]
rs6487815	0.82[AFR][1000 genomes]
rs7297435	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7311742	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7315504	0.82[AFR][1000 genomes]
rs7953619	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9651802	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs966540	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs966541	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs996498	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9989017	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1796867	chr12:29501941-29524159	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10082956	RP11-996F15.2	cis	Artery Tibial	GTEx
rs10082956	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs10082956	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10082956	RP11-996F15.2	cis	Thyroid	GTEx
rs10082956	RP11-996F15.2	cis	Artery Aorta	GTEx
rs10082956	RP11-996F15.2	cis	Stomach	GTEx
rs10082956	RP11-996F15.2	cis	Whole Blood	GTEx
rs10082956	RP11-996F15.2	cis	lung	GTEx
rs10082956	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs10082956	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs10082956	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs10082956	ERGIC2	cis	multi-tissue	Pritchard
rs10082956	RP11-996F15.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
3	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
5	chr12:29473800-29522600	Weak transcription	NHEK	skin
6	chr12:29476200-29509400	Weak transcription	Spleen	Spleen
7	chr12:29476200-29512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
9	chr12:29476400-29509600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:29477000-29517800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:29483400-29518000	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
15	chr12:29485600-29533400	Weak transcription	Gastric	stomach
16	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
17	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:29488800-29532000	Weak transcription	NHLF	lung
19	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:29489800-29510000	Weak transcription	Brain Germinal Matrix	brain
21	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
23	chr12:29490200-29506000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:29491000-29511400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:29491400-29506400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:29492400-29511800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:29492400-29518000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:29492800-29511800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:29492800-29519000	Weak transcription	HepG2	liver
31	chr12:29493200-29504800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:29493600-29532600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:29494400-29517800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:29494400-29532400	Weak transcription	Brain Substantia Nigra	brain
35	chr12:29494600-29509000	Weak transcription	Lung	lung
36	chr12:29494600-29511800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:29494600-29532800	Weak transcription	Colonic Mucosa	Colon
38	chr12:29496400-29509200	Weak transcription	Left Ventricle	heart
39	chr12:29496400-29518000	Weak transcription	Brain Anterior Caudate	brain
40	chr12:29496400-29518000	Weak transcription	Thymus	Thymus
41	chr12:29496400-29532200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:29496600-29517800	Weak transcription	NH-A	brain
43	chr12:29496800-29508600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:29496800-29519000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:29497000-29509000	Weak transcription	HMEC	breast
46	chr12:29497400-29532400	Weak transcription	Fetal Heart	heart
47	chr12:29497600-29518200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:29498000-29515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:29498800-29507800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:29498800-29509000	Weak transcription	Rectal Mucosa Donor 29	rectum

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