Variant report

Variant	rs7647973
Chromosome Location	chr3:49510931-49510932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49508269..49511222-chr3:49551619..49554342,2	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10154992	1.00[ASN][1000 genomes]
rs10155014	0.88[EUR][1000 genomes]
rs10452032	1.00[ASN][1000 genomes]
rs1078341	1.00[ASN][1000 genomes]
rs10865956	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106620	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11130183	1.00[ASN][1000 genomes]
rs11130186	1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	0.86[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	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	0.91[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720705	1.00[ASN][1000 genomes]
rs11923032	0.82[EUR][1000 genomes]
rs11928090	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12583	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs12715437	1.00[ASN][1000 genomes]
rs13096474	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[ASN][1000 genomes]
rs1982861	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.88[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	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312462	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2329021	1.00[ASN][1000 genomes]
rs2329025	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3020779	1.00[ASN][1000 genomes]
rs3448	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3866330	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3870339	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3870341	0.89[EUR][1000 genomes]
rs3905330	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4052546	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4241407	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4384984	1.00[ASN][1000 genomes]
rs4855837	0.87[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];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855858	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855869	0.90[EUR][1000 genomes]
rs4855885	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955424	0.82[EUR][1000 genomes]
rs4955425	0.81[EUR][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	1.00[ASN][1000 genomes]
rs4955443	1.00[ASN][1000 genomes]
rs56049603	0.80[EUR][1000 genomes]
rs56127630	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56324858	0.84[EUR][1000 genomes]
rs57273516	0.94[EUR][1000 genomes]
rs62259933	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62261249	0.90[AMR][1000 genomes];0.89[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]
rs6446257	1.00[ASN][1000 genomes]
rs6446262	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6446275	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6769744	0.85[EUR][1000 genomes]
rs6769821	1.00[ASN][1000 genomes]
rs6775069	0.83[EUR][1000 genomes]
rs6778080	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6783003	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6784203	0.82[EUR][1000 genomes]
rs6785045	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796147	0.81[EUR][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808036	1.00[ASN][1000 genomes]
rs6809204	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934271	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073004	0.80[EUR][1000 genomes]
rs73088137	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7429661	1.00[ASN][1000 genomes]
rs7613491	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619016	1.00[ASN][1000 genomes]
rs7619789	0.94[EUR][1000 genomes]
rs7620024	0.90[EUR][1000 genomes]
rs7622786	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7625857	0.87[EUR][1000 genomes]
rs7626076	1.00[ASN][1000 genomes]
rs7638750	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644148	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7648995	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9654010	0.91[EUR][1000 genomes]
rs974495	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9757181	1.00[CEU][hapmap]
rs9809237	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9817807	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9842132	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9867285	1.00[ASN][1000 genomes]
rs9871024	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	1.00[CEU][hapmap];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

Variant related diseases (count:1)

Disease	PMID	Source
Menarche (age at onset)	25231870	GWAS catalog

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs7647973	AMT	cis	Esophagus Mucosa	GTEx
rs7647973	AMT	cis	Muscle Skeletal	GTEx
rs7647973	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs7647973	AMT	cis	Whole Blood	GTEx
rs7647973	AMT	cis	Adipose Subcutaneous	GTEx
rs7647973	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs7647973	WDR6	cis	Nerve Tibial	GTEx
rs7647973	AMT	cis	Artery Aorta	GTEx
rs7647973	AMT	cis	Nerve Tibial	GTEx
rs7647973	NICN1	cis	Thyroid	GTEx
rs7647973	AMT	cis	lung	GTEx
rs7647973	AMT	cis	Esophagus Muscularis	GTEx
rs7647973	WDR6	cis	Muscle Skeletal	GTEx
rs7647973	AMT	cis	Thyroid	GTEx
rs7647973	ARIH2	cis	Thyroid	GTEx
rs7647973	RHOA	cis	Muscle Skeletal	GTEx
rs7647973	NICN1-AS1	cis	Thyroid	GTEx
rs7647973	AMT	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49508800-49511200	Enhancers	Placenta	Placenta
2	chr3:49509000-49511200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:49509400-49513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:49509400-49514200	Weak transcription	Thymus	Thymus
5	chr3:49509400-49520200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:49509600-49513600	Weak transcription	HUVEC	blood vessel
7	chr3:49509600-49513800	Weak transcription	NH-A	brain
8	chr3:49509600-49514200	Weak transcription	Fetal Brain Female	brain
9	chr3:49509600-49514400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:49509600-49514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:49509600-49519000	Weak transcription	Primary B cells from cord blood	blood
12	chr3:49509600-49522800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:49509600-49530800	Weak transcription	Brain Germinal Matrix	brain
14	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:49509800-49511000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:49509800-49511600	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr3:49509800-49512800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:49509800-49513400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:49509800-49513400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:49509800-49513400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:49509800-49513600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:49509800-49513600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:49509800-49513600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:49509800-49513600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:49509800-49513600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:49509800-49513600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:49509800-49513600	Weak transcription	Osteobl	bone
28	chr3:49509800-49513800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:49509800-49513800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:49509800-49513800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:49509800-49513800	Weak transcription	Adipose Nuclei	Adipose
32	chr3:49509800-49513800	Weak transcription	Esophagus	oesophagus
33	chr3:49509800-49514200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:49509800-49514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:49509800-49514200	Weak transcription	Lung	lung
36	chr3:49509800-49514200	Weak transcription	Spleen	Spleen
37	chr3:49509800-49514200	Weak transcription	A549	lung
38	chr3:49509800-49514400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:49509800-49514600	Weak transcription	Aorta	Aorta
40	chr3:49509800-49514600	Weak transcription	Gastric	stomach
41	chr3:49509800-49514600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:49509800-49514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:49509800-49514800	Weak transcription	Liver	Liver
44	chr3:49509800-49514800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:49509800-49514800	Weak transcription	Colonic Mucosa	Colon
46	chr3:49509800-49514800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:49509800-49520800	Weak transcription	Ovary	ovary
48	chr3:49509800-49522800	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:49509800-49522800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:49509800-49522800	Weak transcription	NHEK	skin

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