Variant report

Variant	rs59906301
Chromosome Location	chr3:49819665-49819666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49816078..49819977-chr3:49822757..49825335,4	MCF-7	breast:
2	chr3:49812806..49814691-chr3:49816470..49819799,3	K562	blood:
3	chr3:49816140..49820070-chr3:49823380..49825359,3	K562	blood:
4	chr3:49816876..49821411-chr3:49821519..49825209,5	K562	blood:

Variant related genes	Relation type
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10049413	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1049256	0.92[ASN][1000 genomes]
rs10865958	0.84[ASN][1000 genomes]
rs10865959	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130214	0.90[ASN][1000 genomes]
rs11130216	0.90[ASN][1000 genomes]
rs11130218	0.89[ASN][1000 genomes]
rs11130219	0.89[ASN][1000 genomes]
rs11130221	0.92[ASN][1000 genomes]
rs1128535	0.84[ASN][1000 genomes]
rs11709680	0.89[ASN][1000 genomes]
rs11710675	0.93[ASN][1000 genomes]
rs11714957	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715304	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11716575	0.89[ASN][1000 genomes]
rs11717256	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11717463	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11920900	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12381242	0.89[ASN][1000 genomes]
rs12490656	0.87[ASN][1000 genomes]
rs12496226	0.85[ASN][1000 genomes]
rs13063621	0.92[ASN][1000 genomes]
rs13084243	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13085679	0.84[ASN][1000 genomes]
rs13086130	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13086465	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13090611	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1317140	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13316065	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1491986	0.89[ASN][1000 genomes]
rs1799843	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1799845	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2234385	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2234391	0.84[ASN][1000 genomes]
rs2246832	0.82[ASN][1000 genomes]
rs2247036	0.82[ASN][1000 genomes]
rs2271960	0.82[ASN][1000 genomes]
rs2271961	0.82[ASN][1000 genomes]
rs2276864	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291542	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2307021	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2352967	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2352974	0.82[ASN][1000 genomes]
rs2352975	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34451146	0.92[ASN][1000 genomes]
rs34522271	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34614773	0.89[ASN][1000 genomes]
rs34735338	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35210174	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35261599	0.94[ASN][1000 genomes]
rs35474403	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749237	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749240	0.92[ASN][1000 genomes]
rs3749241	0.92[ASN][1000 genomes]
rs3811695	0.87[ASN][1000 genomes]
rs3811696	0.89[ASN][1000 genomes]
rs4519692	0.81[ASN][1000 genomes]
rs4768	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4855841	0.86[ASN][1000 genomes]
rs4855850	0.87[ASN][1000 genomes]
rs4855862	0.89[ASN][1000 genomes]
rs4855867	0.89[ASN][1000 genomes]
rs57648519	0.92[ASN][1000 genomes]
rs60205400	0.92[ASN][1000 genomes]
rs62260715	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260719	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62260729	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6446295	0.94[ASN][1000 genomes]
rs6766836	0.92[ASN][1000 genomes]
rs6775384	0.84[ASN][1000 genomes]
rs6785549	0.87[ASN][1000 genomes]
rs6802890	0.89[ASN][1000 genomes]
rs6804655	0.90[ASN][1000 genomes]
rs695238	0.84[ASN][1000 genomes]
rs71324996	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7372725	0.83[ASN][1000 genomes]
rs7372730	0.85[ASN][1000 genomes]
rs7372966	0.83[ASN][1000 genomes]
rs7374183	0.83[ASN][1000 genomes]
rs7374277	0.83[ASN][1000 genomes]
rs7429353	0.83[ASN][1000 genomes]
rs7431078	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431106	0.92[ASN][1000 genomes]
rs7618501	0.93[ASN][1000 genomes]
rs7618519	0.94[ASN][1000 genomes]
rs7629936	0.87[ASN][1000 genomes]
rs7634886	0.89[ASN][1000 genomes]
rs7634902	0.92[ASN][1000 genomes]
rs7645061	0.84[ASN][1000 genomes]
rs7648987	0.84[ASN][1000 genomes]
rs7649348	0.94[ASN][1000 genomes]
rs9814765	0.89[ASN][1000 genomes]
rs9815766	0.92[ASN][1000 genomes]
rs9819511	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9850465	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9853458	0.89[ASN][1000 genomes]
rs9855505	0.83[ASN][1000 genomes]
rs9859153	0.92[ASN][1000 genomes]
rs9865480	0.89[ASN][1000 genomes]
rs9871654	0.91[ASN][1000 genomes]
rs9872864	0.83[ASN][1000 genomes]
rs9873183	0.85[ASN][1000 genomes]
rs9876508	0.94[ASN][1000 genomes]
rs9882639	0.92[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
rs59906301	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs59906301	WDR6	cis	Whole Blood	GTEx

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	chr3:49795000-49821000	Weak transcription	K562	blood
7	chr3:49795400-49822400	Weak transcription	Stomach Mucosa	stomach
8	chr3:49804000-49822600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:49807800-49822600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:49809400-49822800	Weak transcription	A549	lung
11	chr3:49809600-49822400	Weak transcription	NHDF-Ad	bronchial
12	chr3:49810400-49822400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:49812000-49822800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:49812200-49822800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:49812800-49821800	Weak transcription	Fetal Heart	heart
16	chr3:49812800-49822400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:49812800-49822400	Weak transcription	HSMM	muscle
18	chr3:49813200-49822400	Weak transcription	Hela-S3	cervix
19	chr3:49814000-49821800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:49814800-49822400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:49815000-49820400	Weak transcription	Fetal Lung	lung
22	chr3:49815000-49821200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:49815800-49822400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:49816400-49821000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:49816600-49821800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:49816600-49822600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:49817000-49821400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:49817400-49820200	Strong transcription	NHEK	skin
29	chr3:49817400-49822000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr3:49817600-49820400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr3:49817800-49820000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:49817800-49820000	Enhancers	Pancreas	Pancrea
33	chr3:49817800-49820200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:49817800-49820200	Genic enhancers	Dnd41	blood
35	chr3:49817800-49820800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:49817800-49821600	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr3:49817800-49821600	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:49817800-49822000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:49818000-49820000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:49818200-49819800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:49818200-49821800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:49818200-49822200	Strong transcription	Fetal Intestine Large	intestine
43	chr3:49818200-49823200	Weak transcription	Gastric	stomach
44	chr3:49818400-49819800	Weak transcription	Fetal Brain Male	brain
45	chr3:49818400-49820200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr3:49818400-49821200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:49818400-49821400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr3:49818400-49821600	Weak transcription	Right Atrium	heart
49	chr3:49818400-49821600	Weak transcription	GM12878-XiMat	blood
50	chr3:49818400-49821800	Strong transcription	Placenta	Placenta

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