Variant report

Variant	rs10843397
Chromosome Location	chr12:29529523-29529524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:29523685..29526010-chr12:29528444..29531156,2	MCF-7	breast:
2	chr12:29516247..29519208-chr12:29526814..29530124,4	K562	blood:
3	chr12:29519283..29521752-chr12:29527827..29530513,2	K562	blood:
4	chr12:29527046..29529836-chr12:29532806..29534608,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087502	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10082956	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10128781	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1035606	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1035607	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10743657	0.86[AFR][1000 genomes]
rs10743658	0.86[AFR][1000 genomes]
rs10843390	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10843391	0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10843398	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10843403	0.85[AFR][1000 genomes]
rs11050175	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11050203	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1156242	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12320212	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12831751	0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2278093	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2278094	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs3782513	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3815843	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931178	0.86[AFR][1000 genomes]
rs6487815	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7297435	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302557	0.83[AFR][1000 genomes]
rs7311742	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315504	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs7953619	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9651802	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs966540	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9989017	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10843397	RP11-996F15.2	cis	Artery Tibial	GTEx
rs10843397	RP11-996F15.2	cis	Thyroid	GTEx
rs10843397	RP11-996F15.2	cis	lung	GTEx
rs10843397	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs10843397	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10843397	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs10843397	ERGIC2	cis	multi-tissue	Pritchard
rs10843397	RP11-996F15.2	cis	Artery Aorta	GTEx
rs10843397	MLSTD1	cis	normal skin	skin_eQTL
rs10843397	RP11-996F15.2	cis	Stomach	GTEx
rs10843397	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs10843397	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs10843397	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
2	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
3	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
4	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
7	chr12:29485600-29533400	Weak transcription	Gastric	stomach
8	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:29488800-29532000	Weak transcription	NHLF	lung
10	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
12	chr12:29493600-29532600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:29494400-29532400	Weak transcription	Brain Substantia Nigra	brain
14	chr12:29494600-29532800	Weak transcription	Colonic Mucosa	Colon
15	chr12:29496400-29532200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:29497400-29532400	Weak transcription	Fetal Heart	heart
17	chr12:29499000-29532400	Weak transcription	Fetal Brain Female	brain
18	chr12:29500200-29533400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:29503400-29532200	Weak transcription	HSMMtube	muscle
20	chr12:29505000-29532400	Weak transcription	Brain Angular Gyrus	brain
21	chr12:29507600-29532200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:29509400-29529800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:29510200-29532600	Weak transcription	Fetal Stomach	stomach
24	chr12:29510400-29533400	Weak transcription	Lung	lung
25	chr12:29511600-29532200	Weak transcription	HMEC	breast
26	chr12:29515600-29532200	Weak transcription	Fetal Intestine Small	intestine
27	chr12:29516000-29533200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:29518400-29532200	Weak transcription	Brain Anterior Caudate	brain
29	chr12:29518400-29533200	Weak transcription	Ovary	ovary
30	chr12:29518600-29532600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:29518800-29533000	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:29519200-29532000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:29519200-29532800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:29519200-29533000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr12:29519400-29531600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr12:29519400-29531800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:29519400-29532000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:29519400-29532200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:29519400-29532400	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:29520000-29529600	Weak transcription	Fetal Kidney	kidney
41	chr12:29520000-29530000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:29520000-29532600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:29521400-29532400	Weak transcription	HepG2	liver
44	chr12:29522200-29532200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:29522200-29532200	Weak transcription	Brain Germinal Matrix	brain
46	chr12:29522400-29529600	Weak transcription	A549	lung
47	chr12:29522400-29532600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:29522400-29532600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:29522400-29532600	Weak transcription	Fetal Intestine Large	intestine
50	chr12:29522400-29533200	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links