Variant report

Variant	rs7651372
Chromosome Location	chr3:49533931-49533932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1009051	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10154992	1.00[ASN][1000 genomes]
rs10155014	0.85[EUR][1000 genomes]
rs10452032	1.00[ASN][1000 genomes]
rs1078341	1.00[ASN][1000 genomes]
rs10865956	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106620	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11130186	1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	1.00[ASN][1000 genomes]
rs11130217	1.00[ASN][1000 genomes]
rs11709734	1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11715060	0.84[EUR][1000 genomes]
rs11719762	0.82[EUR][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720705	1.00[ASN][1000 genomes]
rs11928090	0.90[EUR][1000 genomes]
rs12583	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs12715437	1.00[ASN][1000 genomes]
rs13096474	0.85[EUR][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	0.88[EUR][1000 genomes]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[ASN][1000 genomes]
rs1982861	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2029591	1.00[ASN][1000 genomes]
rs2082923	1.00[ASN][1000 genomes]
rs2099526	1.00[ASN][1000 genomes]
rs2131108	1.00[ASN][1000 genomes]
rs2140270	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312462	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2329021	1.00[ASN][1000 genomes]
rs2329025	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020779	1.00[ASN][1000 genomes]
rs3448	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3866330	0.90[EUR][1000 genomes]
rs3870339	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3870341	0.90[EUR][1000 genomes]
rs3905330	0.93[EUR][1000 genomes]
rs4052546	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4241407	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4384984	1.00[ASN][1000 genomes]
rs4855837	0.88[EUR][1000 genomes]
rs4855845	1.00[ASN][1000 genomes]
rs4855846	1.00[ASN][1000 genomes]
rs4855848	1.00[ASN][1000 genomes]
rs4855849	1.00[ASN][1000 genomes]
rs4855853	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855858	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4855869	0.87[EUR][1000 genomes]
rs4855885	1.00[ASN][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955443	1.00[ASN][1000 genomes]
rs56127630	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56324858	0.82[EUR][1000 genomes]
rs57273516	0.91[EUR][1000 genomes]
rs62259933	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62261249	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446262	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6446275	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6769744	0.82[EUR][1000 genomes]
rs6775069	0.81[EUR][1000 genomes]
rs6778080	1.00[ASN][1000 genomes]
rs6783003	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6785045	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs72934271	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088137	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7613491	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619016	1.00[ASN][1000 genomes]
rs7619789	0.91[EUR][1000 genomes]
rs7620024	0.87[EUR][1000 genomes]
rs7622786	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7625857	0.88[EUR][1000 genomes]
rs7626076	1.00[ASN][1000 genomes]
rs7638750	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644148	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7647973	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.87[EUR][1000 genomes]
rs9654010	0.88[EUR][1000 genomes]
rs974495	0.82[EUR][1000 genomes]
rs9809237	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9817807	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9842132	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	0.90[EUR][1000 genomes]
rs9871024	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	1.00[ASN][1000 genomes]
rs9883000	1.00[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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7651372	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs7651372	WDR6	cis	Muscle Skeletal	GTEx
rs7651372	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs7651372	AMT	cis	Thyroid	GTEx
rs7651372	AMT	cis	Whole Blood	GTEx
rs7651372	NICN1-AS1	cis	Thyroid	GTEx
rs7651372	AMT	cis	lung	GTEx
rs7651372	AMT	cis	Muscle Skeletal	GTEx
rs7651372	AMT	cis	Artery Aorta	GTEx
rs7651372	AMT	cis	Esophagus Muscularis	GTEx
rs7651372	AMT	cis	Nerve Tibial	GTEx
rs7651372	AMT	cis	Artery Tibial	GTEx
rs7651372	WDR6	cis	Nerve Tibial	GTEx
rs7651372	AMT	cis	Esophagus Mucosa	GTEx
rs7651372	AMT	cis	Adipose Subcutaneous	GTEx
rs7651372	NICN1	cis	Thyroid	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49509800-49537600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:49510000-49535600	Weak transcription	NHLF	lung
5	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:49515000-49535400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:49515400-49547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:49515400-49547800	Weak transcription	Fetal Brain Female	brain
10	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
11	chr3:49516800-49534800	Weak transcription	Liver	Liver
12	chr3:49516800-49537600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:49517000-49547800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:49517200-49547800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:49519400-49535200	Weak transcription	K562	blood
16	chr3:49522200-49547800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:49522400-49537800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:49522400-49548000	Weak transcription	Spleen	Spleen
19	chr3:49523400-49548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:49523400-49548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:49523600-49535200	Weak transcription	Fetal Heart	heart
22	chr3:49523600-49535200	Weak transcription	A549	lung
23	chr3:49523600-49535400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:49523600-49536200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:49523600-49537000	Weak transcription	HMEC	breast
26	chr3:49523600-49537000	Weak transcription	HSMM	muscle
27	chr3:49523600-49537000	Weak transcription	NHDF-Ad	bronchial
28	chr3:49523600-49537600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:49523600-49548200	Weak transcription	Brain Substantia Nigra	brain
30	chr3:49524600-49536200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:49525000-49534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:49526000-49547800	Weak transcription	Dnd41	blood
33	chr3:49526000-49548000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:49526200-49537000	Weak transcription	NHEK	skin
35	chr3:49526200-49537800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:49527600-49535400	Weak transcription	Fetal Intestine Large	intestine
37	chr3:49527600-49535600	Weak transcription	Left Ventricle	heart
38	chr3:49527600-49547800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:49528200-49539600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:49529600-49568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:49530400-49547800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:49531000-49548000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:49531200-49535400	Weak transcription	Hela-S3	cervix
44	chr3:49531200-49538000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:49531200-49547800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:49531400-49536200	Weak transcription	Right Ventricle	heart
47	chr3:49531400-49537000	Weak transcription	Gastric	stomach
48	chr3:49531400-49537000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:49531400-49539600	Weak transcription	Fetal Stomach	stomach
50	chr3:49531400-49547600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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