Variant report

Variant	rs7613491
Chromosome Location	chr3:49508976-49508977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:49506252-49509681	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr3:49508840-49508990	HCPEpiC	choroid plexus:	n/a	n/a
3	HCFC1	chr3:49506744-49509311	Hela-S3	cervix:	n/a	n/a
4	MAX	chr3:49508926-49509162	K562	blood:	n/a	chr3:49509096-49509107
5	MXI1	chr3:49506448-49509224	IMR90	lung:	n/a	n/a
6	MAZ	chr3:49506361-49509347	IMR90	lung:	n/a	chr3:49507013-49507023 chr3:49509096-49509107

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49506494..49510419-chr3:49709515..49713189,4	MCF-7	breast:
2	chr3:49507792..49509395-chr3:49538517..49540372,2	MCF-7	breast:
3	chr3:49506988..49509379-chr3:49529279..49532110,2	MCF-7	breast:
4	chr3:49506481..49509131-chr3:49546764..49549304,2	MCF-7	breast:
5	chr3:49447402..49451449-chr3:49505916..49509646,7	K562	blood:
6	chr3:49506444..49509653-chr3:49710909..49714606,3	K562	blood:
7	chr3:49056423..49060378-chr3:49506507..49510634,4	K562	blood:
8	chr3:49447402..49452044-chr3:49506038..49509646,9	K562	blood:
9	chr16:30536975..30539864-chr3:49506980..49509217,2	MCF-7	breast:
10	chr3:49130007..49132020-chr3:49507888..49509693,2	K562	blood:
11	chr3:49448236..49450769-chr3:49505936..49509558,3	MCF-7	breast:
12	chr3:49448736..49451146-chr3:49507489..49509395,2	MCF-7	breast:
13	chr3:49460325..49461920-chr3:49506460..49509220,2	MCF-7	breast:
14	chr3:49503012..49504721-chr3:49506646..49509185,2	MCF-7	breast:
15	chr3:49507807..49509484-chr3:49555798..49559257,3	MCF-7	breast:
16	chr3:49507938..49509712-chr3:49512685..49515016,2	K562	blood:
17	chr3:49376524..49378988-chr3:49507303..49509521,2	MCF-7	breast:
18	chr3:49508269..49511222-chr3:49551619..49554342,2	K562	blood:
19	chr3:49455358..49458192-chr3:49507443..49509538,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP130	TF binding region
ENSG00000145022	Chromatin interaction
ENSG00000145020	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000169957	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000201301	Chromatin interaction
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs1009051	0.82[AMR][1000 genomes];0.98[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	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106620	0.84[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	0.82[AMR][1000 genomes];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	0.85[EUR][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720705	1.00[ASN][1000 genomes]
rs11923032	0.82[EUR][1000 genomes]
rs11928090	0.90[EUR][1000 genomes]
rs12583	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs12715437	1.00[ASN][1000 genomes]
rs13096474	0.88[EUR][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	0.91[EUR][1000 genomes]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[ASN][1000 genomes]
rs1982861	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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312462	0.90[EUR][1000 genomes]
rs2329021	1.00[ASN][1000 genomes]
rs2329025	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3020779	1.00[ASN][1000 genomes]
rs3448	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3866330	0.90[EUR][1000 genomes]
rs3870339	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3870341	0.90[EUR][1000 genomes]
rs3905330	0.93[EUR][1000 genomes]
rs4052546	0.91[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4241407	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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855858	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4855869	0.90[EUR][1000 genomes]
rs4855885	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	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	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62261249	0.87[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]
rs6446256	1.00[ASN][1000 genomes]
rs6446257	1.00[ASN][1000 genomes]
rs6446262	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6446275	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	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[ASN][1000 genomes]
rs6783003	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[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	0.85[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	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073004	0.80[EUR][1000 genomes]
rs73088137	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7429661	1.00[ASN][1000 genomes]
rs7619016	1.00[ASN][1000 genomes]
rs7619789	0.94[EUR][1000 genomes]
rs7620024	0.90[EUR][1000 genomes]
rs7622786	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7625857	0.88[EUR][1000 genomes]
rs7626076	1.00[ASN][1000 genomes]
rs7638750	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644148	0.96[EUR][1000 genomes]
rs7647973	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.89[EUR][1000 genomes]
rs9654010	0.91[EUR][1000 genomes]
rs974495	0.85[EUR][1000 genomes]
rs9809237	0.95[EUR][1000 genomes]
rs9817807	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9842132	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	0.90[EUR][1000 genomes]
rs9867285	1.00[ASN][1000 genomes]
rs9871024	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9883000	1.00[ASN][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	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
2	esv3420339	chr3:49505548-49510046	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs7613491	WDR6	cis	Nerve Tibial	GTEx
rs7613491	ARIH2	cis	Thyroid	GTEx
rs7613491	AMT	cis	Artery Tibial	GTEx
rs7613491	WDR6	cis	Muscle Skeletal	GTEx
rs7613491	AMT	cis	Esophagus Mucosa	GTEx
rs7613491	AMT	cis	Nerve Tibial	GTEx
rs7613491	AMT	cis	lung	GTEx
rs7613491	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs7613491	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs7613491	NICN1-AS1	cis	Thyroid	GTEx
rs7613491	AMT	cis	Artery Aorta	GTEx
rs7613491	AMT	cis	Adipose Subcutaneous	GTEx
rs7613491	AMT	cis	Muscle Skeletal	GTEx
rs7613491	AMT	cis	Whole Blood	GTEx
rs7613491	AMT	cis	Thyroid	GTEx
rs7613491	RHOA	cis	Muscle Skeletal	GTEx
rs7613491	AMT	cis	Esophagus Muscularis	GTEx
rs7613491	NICN1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49506400-49509200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49506400-49509600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr3:49506800-49509200	Active TSS	Psoas Muscle	Psoas
4	chr3:49507000-49509000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:49507000-49509000	Active TSS	Aorta	Aorta
6	chr3:49507000-49509000	Active TSS	A549	lung
7	chr3:49507200-49509000	Active TSS	Fetal Intestine Small	intestine
8	chr3:49507200-49509200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:49507200-49509200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:49507200-49509200	Active TSS	Left Ventricle	heart
11	chr3:49507400-49509000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:49507400-49509000	Active TSS	HepG2	liver
13	chr3:49507400-49509000	Active TSS	NHDF-Ad	bronchial
14	chr3:49507400-49509200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:49507400-49509200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:49507400-49509200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:49507400-49509200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:49507400-49509200	Active TSS	Fetal Muscle Trunk	muscle
19	chr3:49507400-49509200	Active TSS	Pancreas	Pancrea
20	chr3:49507400-49509200	Active TSS	Right Ventricle	heart
21	chr3:49507400-49509400	Active TSS	HSMM	muscle
22	chr3:49507400-49509400	Active TSS	HSMMtube	muscle
23	chr3:49507600-49509000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:49507800-49509000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr3:49508000-49509000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:49508000-49509200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:49508000-49509200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:49508200-49509000	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr3:49508200-49509000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr3:49508200-49509000	Flanking Active TSS	HUVEC	blood vessel
31	chr3:49508200-49509200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:49508200-49509200	Active TSS	Right Atrium	heart
33	chr3:49508200-49509400	Flanking Active TSS	Dnd41	blood
34	chr3:49508200-49509600	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr3:49508200-49510000	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr3:49508400-49509000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
37	chr3:49508400-49509000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:49508400-49509000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr3:49508400-49509000	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr3:49508400-49509000	Flanking Active TSS	Fetal Lung	lung
41	chr3:49508400-49509200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:49508400-49509200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr3:49508400-49509200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr3:49508400-49509200	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr3:49508400-49509200	Flanking Active TSS	Fetal Brain Male	brain
46	chr3:49508400-49509200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr3:49508400-49509400	Flanking Active TSS	Liver	Liver
48	chr3:49508400-49509400	Weak transcription	Spleen	Spleen
49	chr3:49508400-49509400	Flanking Active TSS	NHEK	skin
50	chr3:49508400-49509600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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