Variant report

Variant	rs6738445
Chromosome Location	chr2:172599615-172599616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10166005	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10167419	0.92[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10174525	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10184866	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10194102	0.92[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10200608	0.96[CEU][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10201419	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10202823	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs10204502	0.81[EUR][1000 genomes]
rs10204622	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10206062	0.91[CEU][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10207085	0.92[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10497374	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10803863	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1113389	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11678984	0.92[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11757	0.92[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11886820	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11897196	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11904009	0.92[CEU][hapmap];0.84[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12053003	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12185567	0.92[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12692970	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12692973	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12692974	0.92[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12692978	0.83[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs13017585	0.84[EUR][1000 genomes]
rs13018768	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13022113	0.91[EUR][1000 genomes]
rs13419987	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13429113	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429409	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474074	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1554166	0.92[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1973706	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292815	0.92[CEU][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2357061	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2674484	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312916	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312918	0.92[CEU][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312921	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs312924	0.92[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs312925	0.91[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34358700	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34542126	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35379278	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35391289	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35549875	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35854280	0.86[EUR][1000 genomes]
rs36057702	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770445	0.87[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770451	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770452	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3795999	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4667693	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667694	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668412	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668414	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433311	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6433314	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66835971	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6705200	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6709156	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6710698	0.96[CEU][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67204065	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721680	0.92[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6722757	0.92[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6724337	0.92[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs6725388	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs6731562	0.83[CEU][hapmap]
rs6745143	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754817	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757773	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6758704	0.91[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6759575	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71013062	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7355523	0.87[EUR][1000 genomes]
rs7355594	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562356	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7572215	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7573003	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7586207	0.91[CEU][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597387	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7604918	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7608403	0.92[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs908670	0.87[CEU][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs908671	0.87[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs973889	0.92[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[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	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
2	nsv522519	chr2:172586567-172600310	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6738445	AC068039.4	cis	Esophagus Mucosa	GTEx
rs6738445	AC068039.4	cis	lung	GTEx
rs6738445	AC068039.4	cis	Muscle Skeletal	GTEx
rs6738445	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs6738445	AC068039.4	cis	Nerve Tibial	GTEx
rs6738445	AC068039.4	cis	Thyroid	GTEx
rs6738445	AC068039.4	cis	Esophagus Muscularis	GTEx
rs6738445	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs6738445	AC068039.4	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:172546600-172602800	Weak transcription	Small Intestine	intestine
3	chr2:172559600-172605200	Weak transcription	Colonic Mucosa	Colon
4	chr2:172561400-172601800	Weak transcription	Fetal Heart	heart
5	chr2:172564200-172610000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:172569000-172618600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:172569800-172611400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:172579800-172611200	Strong transcription	Adipose Nuclei	Adipose
9	chr2:172580200-172611200	Strong transcription	Placenta	Placenta
10	chr2:172580400-172610600	Strong transcription	Fetal Thymus	thymus
11	chr2:172580400-172611400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:172580400-172611400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:172581200-172601800	Weak transcription	Stomach Mucosa	stomach
14	chr2:172581800-172608600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:172581800-172611600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:172584200-172605400	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:172586800-172600600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:172586800-172612000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:172587600-172600000	Weak transcription	Hela-S3	cervix
20	chr2:172587800-172640800	Weak transcription	Psoas Muscle	Psoas
21	chr2:172588400-172601600	Weak transcription	Dnd41	blood
22	chr2:172588400-172601800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:172588400-172617000	Weak transcription	Spleen	Spleen
24	chr2:172588400-172617400	Weak transcription	Gastric	stomach
25	chr2:172588400-172619800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:172588600-172600600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:172588800-172601600	Weak transcription	Right Ventricle	heart
28	chr2:172588800-172617400	Weak transcription	Pancreas	Pancrea
29	chr2:172589000-172599800	Weak transcription	Esophagus	oesophagus
30	chr2:172589200-172601600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:172589200-172608400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:172589600-172617200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:172590000-172601600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:172591000-172611400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:172591400-172600000	Weak transcription	NHLF	lung
36	chr2:172591800-172606000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:172593000-172602800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:172593200-172645000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:172593400-172605800	Strong transcription	Fetal Intestine Large	intestine
40	chr2:172594200-172601400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:172594400-172601600	Weak transcription	HSMMtube	muscle
42	chr2:172595400-172599800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:172595400-172600000	Weak transcription	Brain Angular Gyrus	brain
44	chr2:172595400-172602200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:172595400-172605400	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:172595400-172619000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:172595600-172601600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:172595600-172607400	Weak transcription	Fetal Intestine Small	intestine
49	chr2:172595600-172615600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:172596400-172600800	Strong transcription	Primary T cells from cord blood	blood

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