Variant report

Variant	rs2247036
Chromosome Location	chr3:49882349-49882350
allele	C/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	chr3:49882099-49882473	HepG2	liver:	n/a	n/a
2	MAX	chr3:49881820-49882426	HepG2	liver:	n/a	chr3:49881912-49881922 chr3:49882062-49882073 chr3:49882063-49882073 chr3:49882063-49882073 chr3:49882061-49882074 chr3:49882064-49882073
3	MAX	chr3:49881683-49882514	HepG2	liver:	n/a	chr3:49881912-49881922 chr3:49882062-49882073 chr3:49882063-49882073 chr3:49882063-49882073 chr3:49881768-49881779 chr3:49882061-49882074 chr3:49882064-49882073
4	MYBL2	chr3:49881911-49882434	HepG2	liver:	n/a	n/a
5	FOXA1	chr3:49881835-49882368	HepG2	liver:	n/a	n/a
6	EP300	chr3:49881854-49882411	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49868893..49870758-chr3:49882070..49883892,2	K562	blood:
2	chr3:49882290..49886564-chr3:49889140..49892041,3	K562	blood:

Variant related genes	Relation type
TRAIP	TF binding region

Extended variants
information (count: 109 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10049413	0.98[ASN][1000 genomes]
rs1049256	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10865958	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865959	0.98[ASN][1000 genomes]
rs11130214	0.82[ASN][1000 genomes]
rs11130216	0.82[ASN][1000 genomes]
rs11130218	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130219	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130221	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1128535	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11709680	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710675	0.85[ASN][1000 genomes]
rs11714957	0.87[ASN][1000 genomes]
rs11715304	0.95[ASN][1000 genomes]
rs11716575	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11717256	0.96[ASN][1000 genomes]
rs11717463	0.87[ASN][1000 genomes]
rs11920900	0.86[ASN][1000 genomes]
rs12381242	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12490656	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13063621	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13084243	0.87[ASN][1000 genomes]
rs13085679	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13086130	0.87[ASN][1000 genomes]
rs13086465	0.85[ASN][1000 genomes]
rs13090611	0.81[ASN][1000 genomes]
rs1317140	0.92[ASN][1000 genomes]
rs13316065	0.96[ASN][1000 genomes]
rs1491986	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1799843	0.94[ASN][1000 genomes]
rs1799845	0.94[ASN][1000 genomes]
rs2234385	0.94[ASN][1000 genomes]
rs2234391	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246832	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271960	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271961	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276864	0.98[ASN][1000 genomes]
rs2291542	0.85[ASN][1000 genomes]
rs2307021	0.85[ASN][1000 genomes]
rs2352967	0.96[ASN][1000 genomes]
rs2352974	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352975	0.98[ASN][1000 genomes]
rs34451146	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34522271	0.87[ASN][1000 genomes]
rs34614773	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34735338	0.87[ASN][1000 genomes]
rs35210174	0.87[ASN][1000 genomes]
rs35261599	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35474403	0.87[ASN][1000 genomes]
rs3749237	0.87[ASN][1000 genomes]
rs3749240	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3749241	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811695	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3811696	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3819325	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4519692	0.92[ASN][1000 genomes]
rs4768	0.85[ASN][1000 genomes]
rs4855841	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4855850	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4855862	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4855867	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57648519	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59906301	0.82[ASN][1000 genomes]
rs60205400	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62260715	0.87[ASN][1000 genomes]
rs62260719	0.94[ASN][1000 genomes]
rs62260729	0.98[ASN][1000 genomes]
rs6446295	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766836	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6775384	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785549	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6802890	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6804655	0.82[ASN][1000 genomes]
rs695238	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71324996	0.82[ASN][1000 genomes]
rs7372725	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7372730	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7372966	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7374183	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7374277	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7426497	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7429353	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7431078	0.87[ASN][1000 genomes]
rs7431106	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618501	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7618519	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7629936	0.90[ASN][1000 genomes]
rs7634886	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7634902	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7645061	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7648987	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7649348	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9814765	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9815766	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9819511	0.95[ASN][1000 genomes]
rs9850465	0.90[ASN][1000 genomes]
rs9853458	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9855505	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9859153	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9865480	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9871654	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9872864	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9873183	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9876508	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9882639	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2247036	UBA7	cis	Whole Blood	GTEx
rs2247036	RBM6	cis	Nerve Tibial	GTEx
rs2247036	RBM6	cis	Artery Tibial	GTEx
rs2247036	RBM6	cis	Thyroid	GTEx
rs2247036	RBM6	cis	Esophagus Muscularis	GTEx
rs2247036	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2247036	FAM212A	cis	Esophagus Mucosa	GTEx
rs2247036	RBM6	cis	Whole Blood	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:49863800-49882800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:49864000-49883200	Weak transcription	Colonic Mucosa	Colon
4	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
5	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:49864800-49886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:49865000-49886000	Strong transcription	Dnd41	blood
8	chr3:49865600-49885800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:49865600-49885800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:49869000-49883200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:49869400-49893000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:49870200-49893000	Weak transcription	HSMM	muscle
13	chr3:49871200-49886000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:49873600-49885800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:49873800-49885800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:49874000-49885800	Strong transcription	Thymus	Thymus
17	chr3:49876000-49882800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:49877000-49882400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:49877000-49893000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:49877000-49893400	Weak transcription	HSMMtube	muscle
21	chr3:49877200-49885000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:49877200-49886000	Weak transcription	Stomach Mucosa	stomach
23	chr3:49877200-49893000	Weak transcription	Gastric	stomach
24	chr3:49877200-49893000	Weak transcription	NHDF-Ad	bronchial
25	chr3:49877200-49893200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:49877400-49882600	Weak transcription	Ovary	ovary
27	chr3:49877400-49883000	Weak transcription	Liver	Liver
28	chr3:49877400-49883000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:49877400-49893000	Weak transcription	A549	lung
30	chr3:49877400-49893200	Weak transcription	Lung	lung
31	chr3:49877400-49893200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:49877600-49893200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:49877800-49885800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:49877800-49893000	Weak transcription	Esophagus	oesophagus
35	chr3:49877800-49893000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:49878000-49883800	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:49878000-49886000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:49878200-49884000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:49878400-49885800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:49878600-49883800	Weak transcription	Fetal Lung	lung
41	chr3:49878800-49886000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:49879000-49885600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:49879000-49885800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:49879000-49886000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:49879000-49893000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:49879000-49893000	Weak transcription	NHLF	lung
47	chr3:49879000-49893200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:49879200-49886000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:49879200-49886000	Strong transcription	Fetal Stomach	stomach
50	chr3:49879200-49893000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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