Variant report

Variant	rs908671
Chromosome Location	chr2:172690265-172690266
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172684640..172686879-chr2:172687489..172690776,3	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10166005	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10167419	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]
rs10174055	0.83[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10174525	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10184866	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10194102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10200608	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10201419	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10202823	0.83[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10204502	0.87[AMR][1000 genomes]
rs10204622	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10206062	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10207085	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10432423	0.81[EUR][1000 genomes]
rs10497374	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10803863	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1113389	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11678984	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11757	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11886820	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11897196	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11904009	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12053003	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12185567	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12692970	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12692973	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12692974	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12692978	0.83[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13017585	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13018768	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13022113	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13419987	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13429113	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13429409	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474074	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554166	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1973706	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292815	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2357061	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2674484	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2678155	0.84[AMR][1000 genomes]
rs312916	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs312918	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs312919	0.87[AMR][1000 genomes]
rs312921	0.84[AMR][1000 genomes]
rs312924	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs312925	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34358700	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34542126	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35379278	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35391289	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35549875	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35854280	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36057702	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770445	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770451	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770452	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3795999	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4667693	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4667694	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4668412	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4668414	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6433311	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6433314	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433319	0.83[CEU][hapmap]
rs66835971	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6705200	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709156	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6710698	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67204065	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6721680	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6722757	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6724337	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6725388	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6727017	0.80[CEU][hapmap];0.93[JPT][hapmap]
rs6731562	0.83[CEU][hapmap]
rs6738445	0.87[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6745143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6752812	0.93[JPT][hapmap]
rs6754817	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6757773	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6758704	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6759575	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71013062	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7355523	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7355594	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7562356	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7572215	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7573003	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7586207	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7597387	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7604918	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7608403	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs908670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973889	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[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	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	nsv583611	chr2:172683481-172750257	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs908671	AC068039.4	cis	Thyroid	GTEx
rs908671	AC068039.4	cis	Heart Left Ventricle	GTEx
rs908671	AC068039.4	cis	Nerve Tibial	GTEx
rs908671	SLC25A12	cis	multi-tissue	Pritchard
rs908671	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs908671	AC068039.4	cis	lung	GTEx
rs908671	AC068039.4	cis	Whole Blood	GTEx
rs908671	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs908671	AC068039.4	cis	Stomach	GTEx
rs908671	AC068039.4	cis	Esophagus Muscularis	GTEx
rs908671	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs908671	AC068039.4	cis	Muscle Skeletal	GTEx
rs908671	AC068039.4	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172681000-172695000	Weak transcription	Pancreas	Pancrea
2	chr2:172681800-172693800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:172682000-172694000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr2:172683400-172693800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr2:172683400-172694400	Strong transcription	Primary T cells from cord blood	blood
6	chr2:172683600-172693800	Strong transcription	Left Ventricle	heart
7	chr2:172683800-172694200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:172684400-172694000	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:172684600-172691600	Strong transcription	Ovary	ovary
10	chr2:172685000-172691200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chr2:172685200-172691600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr2:172685400-172691600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
13	chr2:172685600-172693000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:172685600-172694600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:172685600-172694800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:172685800-172690400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:172685800-172691400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
18	chr2:172685800-172694000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:172686000-172694000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:172686200-172691800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
21	chr2:172686200-172698800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:172686800-172693600	Strong transcription	Colon Smooth Muscle	Colon
23	chr2:172687000-172694600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:172687200-172690600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:172687200-172690600	Weak transcription	Liver	Liver
26	chr2:172687200-172692200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:172687200-172693600	Strong transcription	Rectal Smooth Muscle	rectum
28	chr2:172687200-172694000	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:172687400-172690400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
30	chr2:172687400-172690400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr2:172687400-172691200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
32	chr2:172687400-172691200	ZNF genes & repeats	Dnd41	blood
33	chr2:172687400-172691400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
34	chr2:172687400-172691600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:172687400-172691600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:172687400-172691800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:172687400-172693200	Strong transcription	Colonic Mucosa	Colon
38	chr2:172687400-172693400	Strong transcription	HSMMtube	muscle
39	chr2:172687400-172693800	Strong transcription	Brain Anterior Caudate	brain
40	chr2:172687400-172693800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr2:172687400-172693800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr2:172687400-172694000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:172687400-172694000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr2:172687400-172694000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:172687400-172694000	Strong transcription	K562	blood
46	chr2:172687600-172693400	Strong transcription	Brain Hippocampus Middle	brain
47	chr2:172687600-172693600	Strong transcription	Adipose Nuclei	Adipose
48	chr2:172687600-172693800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:172687600-172693800	Strong transcription	Brain Angular Gyrus	brain
50	chr2:172687800-172690600	Strong transcription	Hela-S3	cervix

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