Variant report

Variant	rs13084243
Chromosome Location	chr3:49821878-49821879
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49737567..49739735-chr3:49821150..49823977,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164068	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10049413	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1049256	0.96[ASN][1000 genomes]
rs10865958	0.89[ASN][1000 genomes]
rs10865959	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130214	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130216	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130218	0.94[ASN][1000 genomes]
rs11130219	0.94[ASN][1000 genomes]
rs11130221	0.96[ASN][1000 genomes]
rs1128535	0.89[ASN][1000 genomes]
rs11709680	0.94[ASN][1000 genomes]
rs11710675	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714957	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715304	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11716575	0.94[ASN][1000 genomes]
rs11717256	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11717463	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12381242	0.94[ASN][1000 genomes]
rs12490656	0.92[ASN][1000 genomes]
rs12496226	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13063621	0.96[ASN][1000 genomes]
rs13085679	0.89[ASN][1000 genomes]
rs13086130	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086465	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090611	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1317140	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13316065	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491986	0.94[ASN][1000 genomes]
rs1799843	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1799845	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2234385	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2234391	0.89[ASN][1000 genomes]
rs2246832	0.87[ASN][1000 genomes]
rs2247036	0.87[ASN][1000 genomes]
rs2271960	0.87[ASN][1000 genomes]
rs2271961	0.87[ASN][1000 genomes]
rs2276864	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291542	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307021	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2352967	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2352974	0.87[ASN][1000 genomes]
rs2352975	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34451146	0.96[ASN][1000 genomes]
rs34522271	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34614773	0.94[ASN][1000 genomes]
rs34735338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35210174	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35261599	0.99[ASN][1000 genomes]
rs35474403	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749237	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749240	0.96[ASN][1000 genomes]
rs3749241	0.96[ASN][1000 genomes]
rs3811695	0.92[ASN][1000 genomes]
rs3811696	0.94[ASN][1000 genomes]
rs3819325	0.84[ASN][1000 genomes]
rs4519692	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4855841	0.91[ASN][1000 genomes]
rs4855850	0.92[ASN][1000 genomes]
rs4855862	0.94[ASN][1000 genomes]
rs4855867	0.94[ASN][1000 genomes]
rs57648519	0.96[ASN][1000 genomes]
rs59906301	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60205400	0.96[ASN][1000 genomes]
rs62260715	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62260719	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260729	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446295	0.99[ASN][1000 genomes]
rs6766836	0.96[ASN][1000 genomes]
rs6775384	0.89[ASN][1000 genomes]
rs6785549	0.92[ASN][1000 genomes]
rs6802890	0.94[ASN][1000 genomes]
rs6804655	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs695238	0.89[ASN][1000 genomes]
rs71324996	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7372725	0.88[ASN][1000 genomes]
rs7372730	0.90[ASN][1000 genomes]
rs7372966	0.88[ASN][1000 genomes]
rs7374183	0.88[ASN][1000 genomes]
rs7374277	0.88[ASN][1000 genomes]
rs7429353	0.88[ASN][1000 genomes]
rs7431078	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431106	0.96[ASN][1000 genomes]
rs7618501	0.98[ASN][1000 genomes]
rs7618519	0.99[ASN][1000 genomes]
rs7629936	0.92[ASN][1000 genomes]
rs7634886	0.94[ASN][1000 genomes]
rs7634902	0.96[ASN][1000 genomes]
rs7645061	0.89[ASN][1000 genomes]
rs7648987	0.89[ASN][1000 genomes]
rs7649348	0.99[ASN][1000 genomes]
rs9814765	0.94[ASN][1000 genomes]
rs9815766	0.96[ASN][1000 genomes]
rs9819511	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9850465	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9853458	0.94[ASN][1000 genomes]
rs9855505	0.88[ASN][1000 genomes]
rs9859153	0.96[ASN][1000 genomes]
rs9865480	0.94[ASN][1000 genomes]
rs9871654	0.95[ASN][1000 genomes]
rs9872864	0.88[ASN][1000 genomes]
rs9873183	0.89[ASN][1000 genomes]
rs9876508	0.99[ASN][1000 genomes]
rs9882639	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13084243	WDR6	cis	Whole Blood	GTEx
rs13084243	RBM6	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49785600-49822400	Weak transcription	HSMMtube	muscle
3	chr3:49785600-49822600	Weak transcription	Esophagus	oesophagus
4	chr3:49786000-49823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:49786200-49822400	Weak transcription	HMEC	breast
6	chr3:49795400-49822400	Weak transcription	Stomach Mucosa	stomach
7	chr3:49804000-49822600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:49807800-49822600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:49809400-49822800	Weak transcription	A549	lung
10	chr3:49809600-49822400	Weak transcription	NHDF-Ad	bronchial
11	chr3:49810400-49822400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49812000-49822800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:49812200-49822800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:49812800-49822400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:49812800-49822400	Weak transcription	HSMM	muscle
16	chr3:49813200-49822400	Weak transcription	Hela-S3	cervix
17	chr3:49814800-49822400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:49815800-49822400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:49816600-49822600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:49817400-49822000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:49817800-49822000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:49818200-49822200	Strong transcription	Fetal Intestine Large	intestine
23	chr3:49818200-49823200	Weak transcription	Gastric	stomach
24	chr3:49818400-49822200	Weak transcription	Psoas Muscle	Psoas
25	chr3:49818400-49822200	Strong transcription	Thymus	Thymus
26	chr3:49818400-49822400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:49818400-49822400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:49818600-49822400	Strong transcription	Fetal Intestine Small	intestine
29	chr3:49818600-49822400	Weak transcription	NH-A	brain
30	chr3:49819200-49822000	Weak transcription	Primary B cells from cord blood	blood
31	chr3:49819200-49822200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:49819200-49822400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:49819200-49822400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:49819200-49822400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:49819200-49822400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:49819200-49822400	Weak transcription	Fetal Kidney	kidney
37	chr3:49819200-49822400	Strong transcription	Fetal Thymus	thymus
38	chr3:49819200-49822400	Weak transcription	Small Intestine	intestine
39	chr3:49819200-49822400	Weak transcription	Spleen	Spleen
40	chr3:49819200-49822600	Weak transcription	Colonic Mucosa	Colon
41	chr3:49819200-49823000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:49819200-49823000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:49819200-49823000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:49819400-49822200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:49819400-49822200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:49819400-49822200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:49819400-49822400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:49819400-49822400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:49819400-49822400	Weak transcription	Brain Anterior Caudate	brain
50	chr3:49819400-49822400	Weak transcription	Brain Substantia Nigra	brain

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