Variant report

Variant	rs12496226
Chromosome Location	chr3:49734040-49734041
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49732776-49736804	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49727338..49730126-chr3:49733777..49735933,2	K562	blood:
2	chr3:49725473..49727934-chr3:49733228..49735163,2	MCF-7	breast:

Variant related genes	Relation type
RNF123	TF binding region
ENSG00000173531	Chromatin interaction
ENSG00000164068	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1049256	0.92[ASN][1000 genomes]
rs10865959	0.80[EUR][1000 genomes]
rs11130214	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130216	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130218	0.89[ASN][1000 genomes]
rs11130219	0.89[ASN][1000 genomes]
rs11130221	0.87[ASN][1000 genomes]
rs11709680	0.89[ASN][1000 genomes]
rs11710675	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11714957	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715304	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11716575	0.89[ASN][1000 genomes]
rs11717256	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11717463	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11920900	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12381242	0.89[ASN][1000 genomes]
rs12490656	0.82[ASN][1000 genomes]
rs13063621	0.87[ASN][1000 genomes]
rs13084243	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13086130	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13086465	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13090611	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1491986	0.89[ASN][1000 genomes]
rs1799843	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1799845	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2234385	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291542	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2307021	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2352967	0.81[EUR][1000 genomes]
rs34451146	0.87[ASN][1000 genomes]
rs34522271	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34614773	0.89[ASN][1000 genomes]
rs34735338	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35210174	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35261599	0.89[ASN][1000 genomes]
rs35474403	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3749237	0.96[EUR][1000 genomes];0.90[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]
rs4768	0.90[AMR][1000 genomes];0.97[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	0.87[ASN][1000 genomes]
rs59906301	0.85[ASN][1000 genomes]
rs60205400	0.87[ASN][1000 genomes]
rs62260715	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62260719	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6446295	0.89[ASN][1000 genomes]
rs6766836	0.87[ASN][1000 genomes]
rs6785549	0.92[ASN][1000 genomes]
rs6802890	0.85[ASN][1000 genomes]
rs6804655	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71324996	0.81[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	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7431106	0.87[ASN][1000 genomes]
rs7618501	0.88[ASN][1000 genomes]
rs7618519	0.89[ASN][1000 genomes]
rs7629936	0.82[ASN][1000 genomes]
rs7634886	0.85[ASN][1000 genomes]
rs7634902	0.92[ASN][1000 genomes]
rs7649348	0.89[ASN][1000 genomes]
rs9814765	0.85[ASN][1000 genomes]
rs9815766	0.87[ASN][1000 genomes]
rs9850465	0.82[EUR][1000 genomes]
rs9853458	0.89[ASN][1000 genomes]
rs9855505	0.83[ASN][1000 genomes]
rs9859153	0.87[ASN][1000 genomes]
rs9865480	0.89[ASN][1000 genomes]
rs9871654	0.86[ASN][1000 genomes]
rs9872864	0.83[ASN][1000 genomes]
rs9873183	0.89[ASN][1000 genomes]
rs9876508	0.89[ASN][1000 genomes]
rs9882639	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	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
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv820990	chr3:49720651-49735911	Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv12377	chr3:49720751-49735851	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	nsv822077	chr3:49721400-49734526	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	esv1825475	chr3:49722732-49734243	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12496226	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs12496226	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49727600-49734600	Weak transcription	Aorta	Aorta
2	chr3:49727600-49734600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:49727800-49736200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:49727800-49740000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:49727800-49742200	Weak transcription	Small Intestine	intestine
6	chr3:49728000-49734400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:49728000-49734600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:49728000-49734600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:49728000-49734600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:49728000-49734800	Weak transcription	Osteobl	bone
11	chr3:49728000-49736200	Weak transcription	HSMMtube	muscle
12	chr3:49728000-49737000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:49728000-49738400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:49728000-49738600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:49728000-49738600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:49728000-49739200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:49728000-49739200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:49728000-49739400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:49728000-49742600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:49728000-49744400	Weak transcription	NH-A	brain
21	chr3:49728000-49748800	Weak transcription	A549	lung
22	chr3:49728400-49734400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:49728400-49734400	Weak transcription	Fetal Brain Female	brain
24	chr3:49728400-49734600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:49728400-49734600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:49728400-49735200	Weak transcription	GM12878-XiMat	blood
27	chr3:49728400-49735600	Weak transcription	NHLF	lung
28	chr3:49728400-49736200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:49728400-49753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:49728600-49734200	Weak transcription	NHEK	skin
32	chr3:49728600-49734400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:49728600-49734400	Weak transcription	Fetal Lung	lung
34	chr3:49728600-49734600	Weak transcription	Brain Germinal Matrix	brain
35	chr3:49728600-49734600	Weak transcription	Placenta	Placenta
36	chr3:49728600-49735200	Weak transcription	Stomach Mucosa	stomach
37	chr3:49728600-49736200	Weak transcription	HSMM	muscle
38	chr3:49728600-49739400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:49728600-49744800	Weak transcription	HMEC	breast
40	chr3:49728600-49750400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:49728800-49734400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:49728800-49734400	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:49728800-49734400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:49728800-49734800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:49728800-49735000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:49728800-49735200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr3:49728800-49735400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:49729000-49734200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:49729000-49734400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:49729000-49734400	Weak transcription	Stomach Smooth Muscle	stomach

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