Variant report

Variant	rs11920900
Chromosome Location	chr3:49823024-49823025
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49822915..49825593-chr3:49837367..49840860,3	K562	blood:
2	chr3:49759986..49763114-chr3:49822374..49825754,4	MCF-7	breast:
3	chr3:49822569..49826385-chr3:49827149..49830694,4	MCF-7	breast:
4	chr3:49737567..49739735-chr3:49821150..49823977,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187492	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000173540	Chromatin interaction
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];0.86[ASN][1000 genomes]
rs1049256	0.95[ASN][1000 genomes]
rs10865958	0.88[ASN][1000 genomes]
rs10865959	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130214	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130216	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130218	0.93[ASN][1000 genomes]
rs11130219	0.93[ASN][1000 genomes]
rs11130221	0.95[ASN][1000 genomes]
rs1128535	0.88[ASN][1000 genomes]
rs11709680	0.93[ASN][1000 genomes]
rs11710675	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714957	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715304	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11716575	0.93[ASN][1000 genomes]
rs11717256	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717463	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12381242	0.93[ASN][1000 genomes]
rs12490656	0.90[ASN][1000 genomes]
rs12496226	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13063621	0.95[ASN][1000 genomes]
rs13084243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13085679	0.88[ASN][1000 genomes]
rs13086130	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13086465	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090611	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1317140	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13316065	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491986	0.93[ASN][1000 genomes]
rs1799843	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1799845	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2234385	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2234391	0.90[ASN][1000 genomes]
rs2246832	0.86[ASN][1000 genomes]
rs2247036	0.86[ASN][1000 genomes]
rs2271960	0.86[ASN][1000 genomes]
rs2271961	0.86[ASN][1000 genomes]
rs2276864	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291542	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307021	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2352967	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2352974	0.86[ASN][1000 genomes]
rs2352975	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34451146	0.95[ASN][1000 genomes]
rs34522271	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34614773	0.93[ASN][1000 genomes]
rs34735338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35210174	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35261599	0.98[ASN][1000 genomes]
rs35474403	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749237	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749240	0.95[ASN][1000 genomes]
rs3749241	0.95[ASN][1000 genomes]
rs3811695	0.91[ASN][1000 genomes]
rs3811696	0.93[ASN][1000 genomes]
rs3819325	0.82[ASN][1000 genomes]
rs4519692	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4855841	0.90[ASN][1000 genomes]
rs4855850	0.90[ASN][1000 genomes]
rs4855862	0.93[ASN][1000 genomes]
rs4855867	0.93[ASN][1000 genomes]
rs57648519	0.95[ASN][1000 genomes]
rs59906301	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60205400	0.95[ASN][1000 genomes]
rs62260715	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62260719	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62260729	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6446295	0.98[ASN][1000 genomes]
rs6766836	0.95[ASN][1000 genomes]
rs6775384	0.88[ASN][1000 genomes]
rs6785549	0.91[ASN][1000 genomes]
rs6802890	0.95[ASN][1000 genomes]
rs6804655	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs695238	0.88[ASN][1000 genomes]
rs71324996	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7372725	0.87[ASN][1000 genomes]
rs7372730	0.89[ASN][1000 genomes]
rs7372966	0.87[ASN][1000 genomes]
rs7374183	0.87[ASN][1000 genomes]
rs7374277	0.87[ASN][1000 genomes]
rs7429353	0.87[ASN][1000 genomes]
rs7431078	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7431106	0.95[ASN][1000 genomes]
rs7618501	0.96[ASN][1000 genomes]
rs7618519	0.98[ASN][1000 genomes]
rs7629936	0.93[ASN][1000 genomes]
rs7634886	0.93[ASN][1000 genomes]
rs7634902	0.95[ASN][1000 genomes]
rs7645061	0.88[ASN][1000 genomes]
rs7648987	0.88[ASN][1000 genomes]
rs7649348	0.98[ASN][1000 genomes]
rs9814765	0.93[ASN][1000 genomes]
rs9815766	0.95[ASN][1000 genomes]
rs9819511	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9850465	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9853458	0.93[ASN][1000 genomes]
rs9855505	0.87[ASN][1000 genomes]
rs9859153	0.95[ASN][1000 genomes]
rs9865480	0.93[ASN][1000 genomes]
rs9871654	0.96[ASN][1000 genomes]
rs9872864	0.87[ASN][1000 genomes]
rs9873183	0.88[ASN][1000 genomes]
rs9876508	0.98[ASN][1000 genomes]
rs9882639	0.95[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
rs11920900	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11920900	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	chr3:49818200-49823200	Weak transcription	Gastric	stomach
2	chr3:49819400-49823200	Weak transcription	Aorta	Aorta
3	chr3:49820200-49823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:49821800-49823200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:49822400-49823200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr3:49822400-49823200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr3:49822400-49823200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr3:49822400-49823200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr3:49822400-49823200	Transcr. at gene 5' and 3'	Fetal Lung	lung
10	chr3:49822400-49823200	Enhancers	Small Intestine	intestine
11	chr3:49822400-49823200	Flanking Active TSS	Hela-S3	cervix
12	chr3:49822400-49823200	Flanking Active TSS	NH-A	brain
13	chr3:49822400-49823400	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr3:49822400-49823400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr3:49822400-49823400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:49822400-49823400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr3:49822400-49823400	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr3:49822400-49823400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:49822400-49823400	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr3:49822400-49823600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr3:49822400-49823600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:49822400-49823600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:49822400-49823600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr3:49822400-49824200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:49822400-49824400	Active TSS	Ovary	ovary
26	chr3:49822400-49824600	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:49822600-49823200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:49822600-49823200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr3:49822600-49823400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr3:49822600-49823400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr3:49822600-49823400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr3:49822600-49823400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:49822600-49823400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr3:49822600-49823400	Flanking Active TSS	HSMM	muscle
35	chr3:49822600-49823400	Flanking Active TSS	HUVEC	blood vessel
36	chr3:49822600-49823400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr3:49822600-49823600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:49822600-49823600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:49822600-49824200	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr3:49822600-49824200	Active TSS	Rectal Smooth Muscle	rectum
41	chr3:49822600-49824200	Active TSS	HSMMtube	muscle
42	chr3:49822600-49824400	Active TSS	H1 Cell Line	embryonic stem cell
43	chr3:49822600-49824400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:49822600-49824400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:49822600-49824400	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr3:49822600-49824400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:49822600-49824400	Active TSS	Brain Anterior Caudate	brain
48	chr3:49822600-49824400	Active TSS	Brain Cingulate Gyrus	brain
49	chr3:49822600-49824400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:49822600-49824400	Active TSS	Pancreatic Islets	Pancreatic Islet

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