Variant report

Variant	rs9873183
Chromosome Location	chr3:49734229-49734230
allele	A/G
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
ENSG00000164068	Chromatin interaction
ENSG00000173531	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1049256	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10865958	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130214	0.94[ASN][1000 genomes]
rs11130216	0.94[ASN][1000 genomes]
rs11130218	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130219	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130221	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1128535	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11709680	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11710675	0.92[ASN][1000 genomes]
rs11714957	0.89[ASN][1000 genomes]
rs11715304	0.84[ASN][1000 genomes]
rs11716575	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11717256	0.85[ASN][1000 genomes]
rs11717463	0.89[ASN][1000 genomes]
rs11920900	0.88[ASN][1000 genomes]
rs12381242	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12490656	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12496226	0.89[ASN][1000 genomes]
rs13063621	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13084243	0.89[ASN][1000 genomes]
rs13085679	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13086130	0.89[ASN][1000 genomes]
rs13086465	0.87[ASN][1000 genomes]
rs13090611	0.86[ASN][1000 genomes]
rs13316065	0.80[ASN][1000 genomes]
rs1491986	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1799843	0.83[ASN][1000 genomes]
rs1799845	0.83[ASN][1000 genomes]
rs2234385	0.83[ASN][1000 genomes]
rs2234391	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2246832	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2247036	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2271960	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2271961	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291542	0.92[ASN][1000 genomes]
rs2307021	0.92[ASN][1000 genomes]
rs2352967	0.80[ASN][1000 genomes]
rs2352974	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34451146	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34522271	0.89[ASN][1000 genomes]
rs34614773	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34735338	0.87[ASN][1000 genomes]
rs35210174	0.89[ASN][1000 genomes]
rs35261599	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35474403	0.89[ASN][1000 genomes]
rs3749237	0.89[ASN][1000 genomes]
rs3749240	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749241	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811695	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3811696	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3819325	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4768	0.92[ASN][1000 genomes]
rs4855841	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4855850	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855862	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4855867	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57648519	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59906301	0.85[ASN][1000 genomes]
rs60205400	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62260715	0.87[ASN][1000 genomes]
rs62260719	0.83[ASN][1000 genomes]
rs6446295	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766836	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6775384	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6785549	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6802890	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804655	0.94[ASN][1000 genomes]
rs695238	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7372725	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372730	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7372966	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7374183	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7374277	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7426497	0.86[AMR][1000 genomes]
rs7429353	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431078	0.89[ASN][1000 genomes]
rs7431106	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618501	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7618519	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7629936	0.81[ASN][1000 genomes]
rs7634886	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7634902	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7645061	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7648987	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7649348	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9814765	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9815766	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9853458	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9855505	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859153	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9865480	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9871654	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9872864	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9876508	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9882639	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9873183	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9873183	FAM212A	cis	Esophagus Mucosa	GTEx
rs9873183	RBM6	cis	lung	GTEx
rs9873183	RBM6	cis	Thyroid	GTEx
rs9873183	UBA7	cis	Whole Blood	GTEx
rs9873183	RBM6	cis	Artery Tibial	GTEx
rs9873183	RBM6	cis	Esophagus Muscularis	GTEx
rs9873183	RBM6	cis	Whole Blood	GTEx
rs9873183	RBM6	cis	Nerve Tibial	GTEx
rs9873183	UBA7	cis	Esophagus Mucosa	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	chr3:49728600-49734400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:49728600-49734400	Weak transcription	Fetal Lung	lung
33	chr3:49728600-49734600	Weak transcription	Brain Germinal Matrix	brain
34	chr3:49728600-49734600	Weak transcription	Placenta	Placenta
35	chr3:49728600-49735200	Weak transcription	Stomach Mucosa	stomach
36	chr3:49728600-49736200	Weak transcription	HSMM	muscle
37	chr3:49728600-49739400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:49728600-49744800	Weak transcription	HMEC	breast
39	chr3:49728600-49750400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:49728800-49734400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:49728800-49734400	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:49728800-49734400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:49728800-49734800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:49728800-49735000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:49728800-49735200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:49728800-49735400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:49729000-49734400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:49729000-49734400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:49729000-49734800	Weak transcription	Primary B cells from cord blood	blood
50	chr3:49729000-49734800	Weak transcription	Colon Smooth Muscle	Colon

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