Variant report

Variant	rs10167419
Chromosome Location	chr2:172649826-172649827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr2:172649543-172650037	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:172648009..172650848-chr2:172967323..172968978,2	MCF-7	breast:
2	chr2:172649118..172653005-chr2:172653047..172656118,3	K562	blood:
3	chr2:172637502..172642511-chr2:172648363..172652969,5	K562	blood:

Variant related genes	Relation type
SLC25A12	TF binding region
ENSG00000115844	Chromatin interaction
ENSG00000236651	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10166005	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10174525	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184866	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10194102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10200608	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10201419	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10202823	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10204502	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10204622	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10207085	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10432423	0.81[EUR][1000 genomes]
rs10497374	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10803863	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1113389	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886820	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11897196	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11904009	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12053003	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12185567	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12692970	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12692973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12692974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692978	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13017585	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13018768	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13022113	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13419987	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13429113	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13429409	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474074	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554166	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1973706	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292815	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2357061	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2674484	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2678155	0.87[AMR][1000 genomes]
rs312916	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs312918	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs312919	0.84[AMR][1000 genomes]
rs312921	0.83[EUR][1000 genomes]
rs312924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34358700	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34542126	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35379278	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35391289	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35549875	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35854280	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36057702	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770445	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795999	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4667693	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4667694	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4668412	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4668414	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433311	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433314	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433319	0.87[CEU][hapmap]
rs66835971	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705200	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709156	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6710698	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67204065	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6722757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6724337	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6725388	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6727017	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs6731562	0.87[CEU][hapmap]
rs6738445	0.92[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757773	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6758704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71013062	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7355523	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7355594	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562356	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7572215	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7573003	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7586207	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7604918	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7608403	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs908670	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs908671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs973889	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10167419	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs10167419	AC068039.4	cis	Esophagus Muscularis	GTEx
rs10167419	AC068039.4	cis	Muscle Skeletal	GTEx
rs10167419	AC068039.4	cis	Stomach	GTEx
rs10167419	AC068039.4	cis	Heart Left Ventricle	GTEx
rs10167419	AC068039.4	cis	Thyroid	GTEx
rs10167419	SLC25A12	cis	multi-tissue	Pritchard
rs10167419	AC068039.4	cis	Nerve Tibial	GTEx
rs10167419	AC068039.4	cis	Esophagus Mucosa	GTEx
rs10167419	AC068039.4	cis	lung	GTEx
rs10167419	AC068039.4	cis	Whole Blood	GTEx
rs10167419	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs10167419	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172603000-172688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:172610200-172651400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:172635400-172654800	Weak transcription	A549	lung
4	chr2:172635600-172654600	Weak transcription	Liver	Liver
5	chr2:172636800-172654800	Weak transcription	Small Intestine	intestine
6	chr2:172638000-172650200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:172638600-172650600	Strong transcription	Stomach Smooth Muscle	stomach
8	chr2:172638800-172650400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:172638800-172650800	Strong transcription	Primary T cells from cord blood	blood
10	chr2:172638800-172650800	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:172638800-172651000	Strong transcription	Dnd41	blood
12	chr2:172639200-172650200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:172639200-172650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:172639800-172650200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:172639800-172650600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:172640000-172650400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:172640000-172650400	Strong transcription	Fetal Thymus	thymus
18	chr2:172640000-172651400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:172640200-172650400	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:172640200-172650600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:172640200-172651000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:172640200-172662800	Weak transcription	Fetal Brain Male	brain
23	chr2:172640400-172668000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:172640600-172650600	Strong transcription	Left Ventricle	heart
25	chr2:172641000-172650400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:172641000-172650400	Strong transcription	Fetal Stomach	stomach
27	chr2:172641600-172666400	Weak transcription	Fetal Kidney	kidney
28	chr2:172642200-172651400	Weak transcription	Fetal Heart	heart
29	chr2:172642200-172651400	Weak transcription	Fetal Intestine Large	intestine
30	chr2:172642200-172654000	Weak transcription	HUVEC	blood vessel
31	chr2:172642200-172654600	Weak transcription	NHEK	skin
32	chr2:172642200-172654800	Weak transcription	HSMM	muscle
33	chr2:172642200-172663600	Weak transcription	K562	blood
34	chr2:172642200-172665800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr2:172642400-172688400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr2:172643600-172687800	Weak transcription	Hela-S3	cervix
37	chr2:172643800-172674600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:172644000-172650400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:172644000-172667000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:172644200-172666600	Weak transcription	Placenta	Placenta
41	chr2:172644400-172654800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:172644400-172655000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:172644400-172655000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:172644400-172656000	Weak transcription	Aorta	Aorta
45	chr2:172644400-172666000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:172644400-172681800	Weak transcription	Brain Substantia Nigra	brain
47	chr2:172644400-172684400	Weak transcription	Spleen	Spleen
48	chr2:172644600-172654400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:172644600-172654400	Weak transcription	NH-A	brain
50	chr2:172644600-172654800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links