Variant report

Variant	rs10201419
Chromosome Location	chr2:172615870-172615871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10166005	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10167419	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10174525	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10184866	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10194102	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10200608	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10204502	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10204622	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10206062	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10207085	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10497374	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10803863	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1113389	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11678984	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11757	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11886820	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11897196	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11904009	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12053003	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12185567	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12692970	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12692973	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12692974	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12692978	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13017585	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13018768	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13022113	0.88[EUR][1000 genomes]
rs13419987	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13429113	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13429409	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474074	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1554166	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1973706	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292815	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2357061	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2674484	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2678155	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs312916	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs312918	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs312919	0.81[AMR][1000 genomes]
rs312921	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs312924	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs312925	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34358700	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34542126	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35379278	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35391289	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35549875	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35645520	0.83[AMR][1000 genomes]
rs35854280	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36057702	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770445	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770451	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770452	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3795999	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4667693	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667694	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4668412	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668414	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433311	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6433314	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66835971	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6705200	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6709156	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6710698	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67204065	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721680	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6722757	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6724337	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6738445	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6745143	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754817	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757773	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6758704	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6759575	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71013062	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7355523	0.84[EUR][1000 genomes]
rs7355594	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562356	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7572215	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7586207	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597387	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7604918	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7608403	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs908670	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs908671	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs973889	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10201419	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs10201419	AC068039.4	cis	Heart Left Ventricle	GTEx
rs10201419	AC068039.4	cis	Whole Blood	GTEx
rs10201419	AC068039.4	cis	Esophagus Muscularis	GTEx
rs10201419	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs10201419	AC068039.4	cis	Thyroid	GTEx
rs10201419	AC068039.4	cis	lung	GTEx
rs10201419	AC068039.4	cis	Stomach	GTEx
rs10201419	AC068039.4	cis	Esophagus Mucosa	GTEx
rs10201419	AC068039.4	cis	Nerve Tibial	GTEx
rs10201419	AC068039.4	cis	Muscle Skeletal	GTEx
rs10201419	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172569000-172618600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:172587800-172640800	Weak transcription	Psoas Muscle	Psoas
3	chr2:172588400-172617000	Weak transcription	Spleen	Spleen
4	chr2:172588400-172617400	Weak transcription	Gastric	stomach
5	chr2:172588400-172619800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:172588800-172617400	Weak transcription	Pancreas	Pancrea
7	chr2:172589600-172617200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:172593200-172645000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:172595400-172619000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:172602000-172624200	Weak transcription	Esophagus	oesophagus
11	chr2:172602600-172621800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:172603000-172616800	Weak transcription	Right Ventricle	heart
13	chr2:172603000-172688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:172603200-172617200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:172603200-172617400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:172603200-172617400	Weak transcription	Lung	lung
17	chr2:172603200-172618400	Weak transcription	Stomach Mucosa	stomach
18	chr2:172603400-172617200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:172603400-172621200	Weak transcription	Small Intestine	intestine
20	chr2:172604400-172617200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:172604400-172617200	Weak transcription	Brain Angular Gyrus	brain
22	chr2:172604400-172618600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr2:172604400-172641200	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:172605200-172617800	Weak transcription	Dnd41	blood
25	chr2:172605600-172617400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:172605600-172622400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:172605800-172620600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:172606000-172617400	Weak transcription	Colonic Mucosa	Colon
29	chr2:172606200-172620000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:172606400-172619400	Weak transcription	NHEK	skin
31	chr2:172607400-172616600	Weak transcription	Fetal Heart	heart
32	chr2:172607400-172627000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:172607600-172618800	Weak transcription	Fetal Kidney	kidney
34	chr2:172607600-172619200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:172607800-172617400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:172607800-172617400	Weak transcription	Thymus	Thymus
37	chr2:172608200-172617000	Weak transcription	Fetal Stomach	stomach
38	chr2:172608400-172617200	Weak transcription	Primary B cells from cord blood	blood
39	chr2:172608800-172616400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:172608800-172617200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:172608800-172617200	Weak transcription	Aorta	Aorta
42	chr2:172608800-172618400	Weak transcription	GM12878-XiMat	blood
43	chr2:172608800-172619600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:172609000-172618000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:172609000-172622200	Weak transcription	Fetal Brain Male	brain
46	chr2:172609200-172620400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr2:172609600-172617200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:172609600-172617400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:172609600-172628800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:172609800-172616600	Weak transcription	Brain Germinal Matrix	brain

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