Variant report

Variant	rs10843390
Chromosome Location	chr12:29496991-29496992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10082956	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]
rs10128781	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1035606	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743657	0.82[AFR][1000 genomes]
rs10743658	0.82[AFR][1000 genomes]
rs10843391	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843397	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10843398	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs10843403	0.83[AFR][1000 genomes]
rs11050175	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs11050203	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11050209	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1156242	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12320212	0.82[EUR][1000 genomes]
rs12831751	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278093	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278094	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3782513	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3815843	0.88[YRI][hapmap];0.84[AMR][1000 genomes]
rs4931178	0.82[AFR][1000 genomes]
rs6487815	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7297435	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7311742	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7315504	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs7953619	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9651802	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs966540	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs966541	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996498	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9989017	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10843390	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs10843390	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs10843390	MLSTD1	cis	normal skin	skin_eQTL
rs10843390	ERGIC2	cis	multi-tissue	Pritchard
rs10843390	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs10843390	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs10843390	RP11-996F15.2	cis	lung	GTEx
rs10843390	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10843390	RP11-996F15.2	cis	Stomach	GTEx
rs10843390	RP11-996F15.2	cis	Artery Tibial	GTEx
rs10843390	RP11-996F15.2	cis	Thyroid	GTEx
rs10843390	RP11-996F15.2	cis	Whole Blood	GTEx
rs10843390	RP11-996F15.2	cis	Artery Aorta	GTEx
rs10843390	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	chr12:29470000-29500000	Weak transcription	K562	blood
4	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
6	chr12:29473800-29522600	Weak transcription	NHEK	skin
7	chr12:29476000-29502600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:29476200-29509400	Weak transcription	Spleen	Spleen
9	chr12:29476200-29512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
11	chr12:29476400-29498600	Weak transcription	Ovary	ovary
12	chr12:29476400-29509600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:29476600-29499200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:29477000-29517800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:29482000-29497200	Weak transcription	Brain Angular Gyrus	brain
18	chr12:29482200-29501400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:29483400-29518000	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
21	chr12:29485600-29533400	Weak transcription	Gastric	stomach
22	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
23	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:29487800-29501400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:29488600-29503800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:29488800-29532000	Weak transcription	NHLF	lung
27	chr12:29489200-29498800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:29489600-29497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:29489600-29500000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:29489800-29510000	Weak transcription	Brain Germinal Matrix	brain
32	chr12:29490000-29502800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
35	chr12:29490200-29502000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr12:29490200-29502200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:29490200-29506000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:29490400-29500600	Strong transcription	Dnd41	blood
39	chr12:29490400-29502800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:29490600-29502000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:29490600-29503000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr12:29491000-29499200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:29491000-29511400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:29491200-29501000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:29491200-29502600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:29491400-29506400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:29491600-29498400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:29492200-29502800	Strong transcription	Placenta	Placenta
50	chr12:29492400-29502000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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