Variant report

Variant	rs7638750
Chromosome Location	chr3:49452957-49452958
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:49452950-49453358	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr3:49452855-49454130	HepG2	liver:	n/a	n/a
3	RAD21	chr3:49452866-49453509	HCT-116	colon:	n/a	n/a
4	MTA3	chr3:49452886-49454772	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:49452636-49452970	HepG2	liver:	n/a	n/a
6	CTCF	chr3:49452949-49453295	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr3:49452940-49453377	HepG2	liver:	n/a	n/a
8	NFIC	chr3:49452877-49453402	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr3:49452933-49454144	GM12892	blood:	n/a	n/a
10	POLR2A	chr3:49452880-49453328	HCT-116	colon:	n/a	n/a
11	RAD21	chr3:49452895-49453452	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:49452801-49454197	GM12878	blood:	n/a	n/a
13	CTCF	chr3:49452939-49453488	A549	lung:	n/a	n/a
14	RAD21	chr3:49452955-49453331	H1-hESC	embryonic stem cell:	n/a	n/a
15	NFIC	chr3:49452889-49453450	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr3:49452820-49453212	GM12878	blood:	n/a	n/a
17	CTCF	chr3:49452900-49453050	NB4	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49452694..49453465-chr3:49486179..49487146,3	MCF-7	breast:
2	chr3:49452077..49454427-chr3:49496570..49500540,3	MCF-7	breast:

No data

Variant related genes	Relation type
RHOA	TF binding region

Extended variants
information (count: 128 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1009051	0.82[EUR][1000 genomes]
rs10154992	1.00[ASN][1000 genomes]
rs10155014	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10452032	1.00[ASN][1000 genomes]
rs1078341	1.00[ASN][1000 genomes]
rs10865956	1.00[ASN][1000 genomes]
rs1106620	0.85[EUR][1000 genomes]
rs11130183	1.00[ASN][1000 genomes]
rs11130186	1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[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]
rs11710434	1.00[ASN][1000 genomes]
rs11715060	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11719762	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs13096474	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[ASN][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	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329021	1.00[ASN][1000 genomes]
rs2329025	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3020779	1.00[ASN][1000 genomes]
rs3448	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs3870339	0.82[EUR][1000 genomes]
rs3905330	0.81[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4384984	1.00[ASN][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	1.00[ASN][1000 genomes]
rs4855858	0.82[EUR][1000 genomes]
rs4855869	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4855885	1.00[ASN][1000 genomes]
rs4955413	0.82[EUR][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955421	1.00[ASN][1000 genomes]
rs4955423	1.00[ASN][1000 genomes]
rs4955424	0.83[EUR][1000 genomes]
rs4955425	0.83[EUR][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	1.00[ASN][1000 genomes]
rs4955443	1.00[ASN][1000 genomes]
rs56127630	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57273516	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62259933	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446256	1.00[ASN][1000 genomes]
rs6446257	1.00[ASN][1000 genomes]
rs6446262	0.86[EUR][1000 genomes]
rs6446275	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6769744	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6769821	1.00[ASN][1000 genomes]
rs6775069	0.85[EUR][1000 genomes]
rs6778080	1.00[ASN][1000 genomes]
rs6783003	0.83[EUR][1000 genomes]
rs6784203	0.83[EUR][1000 genomes]
rs6785045	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796147	0.82[EUR][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808036	1.00[ASN][1000 genomes]
rs6809204	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934271	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088137	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.81[EUR][1000 genomes]
rs7429661	1.00[ASN][1000 genomes]
rs7613491	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617480	1.00[ASN][1000 genomes]
rs7619016	1.00[ASN][1000 genomes]
rs7619789	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7620024	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7626076	1.00[ASN][1000 genomes]
rs7631586	1.00[ASN][1000 genomes]
rs7644148	0.80[EUR][1000 genomes]
rs7647973	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9586	1.00[ASN][1000 genomes]
rs9654010	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs974495	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9809237	0.81[EUR][1000 genomes]
rs9817807	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9831648	1.00[ASN][1000 genomes]
rs9834003	1.00[ASN][1000 genomes]
rs9842132	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867285	1.00[ASN][1000 genomes]
rs9871024	0.82[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7638750	AMT	cis	Esophagus Mucosa	GTEx
rs7638750	AMT	cis	Esophagus Muscularis	GTEx
rs7638750	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs7638750	AMT	cis	Artery Aorta	GTEx
rs7638750	AMT	cis	lung	GTEx
rs7638750	AMT	cis	Muscle Skeletal	GTEx
rs7638750	AMT	cis	Thyroid	GTEx
rs7638750	WDR6	cis	Nerve Tibial	GTEx
rs7638750	AMT	cis	Artery Tibial	GTEx
rs7638750	AMT	cis	Nerve Tibial	GTEx
rs7638750	NICN1	cis	Thyroid	GTEx
rs7638750	NICN1-AS1	cis	Thyroid	GTEx
rs7638750	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs7638750	AMT	cis	Whole Blood	GTEx
rs7638750	WDR6	cis	Muscle Skeletal	GTEx
rs7638750	AMT	cis	Adipose Subcutaneous	GTEx
rs7638750	WDR6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49450400-49459000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49450400-49459400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49450600-49453200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:49450600-49453800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:49450600-49453800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:49450600-49454400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:49450600-49454600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:49450600-49459000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:49450800-49453200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:49450800-49453400	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr3:49450800-49453600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:49450800-49453800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:49450800-49454000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:49450800-49454200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:49450800-49454400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:49450800-49455400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:49450800-49457800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:49450800-49459000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:49450800-49459200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:49450800-49459200	Genic enhancers	Placenta	Placenta
21	chr3:49451000-49453200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr3:49451000-49453600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:49451000-49454400	Weak transcription	Fetal Kidney	kidney
24	chr3:49451000-49458000	Weak transcription	Small Intestine	intestine
25	chr3:49451200-49453000	Weak transcription	Brain Substantia Nigra	brain
26	chr3:49451200-49453000	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:49451200-49453000	Weak transcription	Hela-S3	cervix
28	chr3:49451200-49453000	Weak transcription	HUVEC	blood vessel
29	chr3:49451200-49453200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:49451200-49453200	Weak transcription	Right Atrium	heart
31	chr3:49451200-49453400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:49451200-49455000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:49451200-49459000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:49451200-49459400	Weak transcription	Fetal Brain Male	brain
35	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
36	chr3:49451400-49453200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:49451400-49453200	Strong transcription	Brain Cingulate Gyrus	brain
38	chr3:49451400-49453200	Strong transcription	Fetal Stomach	stomach
39	chr3:49451400-49453600	Weak transcription	Fetal Lung	lung
40	chr3:49451400-49454200	Weak transcription	K562	blood
41	chr3:49451400-49454600	Weak transcription	Fetal Heart	heart
42	chr3:49451400-49459400	Weak transcription	Ovary	ovary
43	chr3:49451600-49453000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:49451600-49453200	Strong transcription	Right Ventricle	heart
45	chr3:49451600-49454600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:49451600-49458000	Strong transcription	NHLF	lung
47	chr3:49451600-49458200	Strong transcription	Fetal Intestine Small	intestine
48	chr3:49451800-49455600	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr3:49452000-49453000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:49452000-49453000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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