Variant report

Variant	rs7374277
Chromosome Location	chr3:49784777-49784778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49782178..49785035-chr3:49823443..49825758,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10049413	0.82[ASN][1000 genomes]
rs1049256	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10865958	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10865959	0.82[ASN][1000 genomes]
rs11130214	0.88[ASN][1000 genomes]
rs11130216	0.88[ASN][1000 genomes]
rs11130218	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130219	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130221	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1128535	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11709680	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11710675	0.86[ASN][1000 genomes]
rs11714957	0.88[ASN][1000 genomes]
rs11715304	0.84[ASN][1000 genomes]
rs11716575	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11717256	0.86[ASN][1000 genomes]
rs11717463	0.88[ASN][1000 genomes]
rs11920900	0.87[ASN][1000 genomes]
rs12381242	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490656	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12496226	0.83[ASN][1000 genomes]
rs13063621	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13084243	0.88[ASN][1000 genomes]
rs13085679	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086130	0.88[ASN][1000 genomes]
rs13086465	0.86[ASN][1000 genomes]
rs13090611	0.96[ASN][1000 genomes]
rs13316065	0.81[ASN][1000 genomes]
rs1491986	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1799843	0.83[ASN][1000 genomes]
rs1799845	0.83[ASN][1000 genomes]
rs2234385	0.83[ASN][1000 genomes]
rs2234391	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2246832	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2247036	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271960	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271961	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2276864	0.82[ASN][1000 genomes]
rs2291542	0.86[ASN][1000 genomes]
rs2307021	0.86[ASN][1000 genomes]
rs2352967	0.81[ASN][1000 genomes]
rs2352974	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2352975	0.82[ASN][1000 genomes]
rs34451146	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34522271	0.88[ASN][1000 genomes]
rs34614773	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34735338	0.88[ASN][1000 genomes]
rs35210174	0.88[ASN][1000 genomes]
rs35261599	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35474403	0.88[ASN][1000 genomes]
rs3749237	0.88[ASN][1000 genomes]
rs3749240	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3749241	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3811695	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3811696	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3819325	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4768	0.86[ASN][1000 genomes]
rs4855841	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855850	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4855862	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4855867	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57648519	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59906301	0.83[ASN][1000 genomes]
rs60205400	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62260715	0.88[ASN][1000 genomes]
rs62260719	0.83[ASN][1000 genomes]
rs62260729	0.82[ASN][1000 genomes]
rs6446295	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6766836	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6775384	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6785549	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6802890	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6804655	0.88[ASN][1000 genomes]
rs695238	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372725	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7372730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7372966	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374183	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7426497	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7429353	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431078	0.88[ASN][1000 genomes]
rs7431106	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618501	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7618519	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7629936	0.82[ASN][1000 genomes]
rs7634886	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7634902	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7645061	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7648987	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7649348	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9814765	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9815766	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9853458	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9855505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859153	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9865480	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9871654	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9872864	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873183	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9876508	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9882639	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7374277	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs7374277	RBM6	cis	Thyroid	GTEx
rs7374277	RBM6	cis	Nerve Tibial	GTEx
rs7374277	RBM6	cis	lung	GTEx
rs7374277	RBM6	cis	Artery Tibial	GTEx
rs7374277	RBM6	cis	Esophagus Muscularis	GTEx
rs7374277	RBM6	cis	Whole Blood	GTEx
rs7374277	FAM212A	cis	Esophagus Mucosa	GTEx
rs7374277	RBM6	cis	Adipose Subcutaneous	GTEx
rs7374277	UBA7	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49762600-49785200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:49762600-49809000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:49763000-49784800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:49765800-49785800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:49767600-49787800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr3:49768200-49787600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr3:49772600-49785400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:49772600-49791600	Weak transcription	Right Atrium	heart
9	chr3:49774000-49788200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:49775600-49788200	Weak transcription	Stomach Mucosa	stomach
11	chr3:49775600-49817000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:49775800-49810200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:49776000-49785200	Weak transcription	GM12878-XiMat	blood
15	chr3:49776000-49789400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:49776000-49791200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:49776000-49791800	Weak transcription	Psoas Muscle	Psoas
18	chr3:49776200-49784800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:49776200-49784800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:49776200-49784800	Weak transcription	Aorta	Aorta
21	chr3:49776200-49784800	Weak transcription	Liver	Liver
22	chr3:49776200-49784800	Weak transcription	Brain Germinal Matrix	brain
23	chr3:49776200-49784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:49776200-49785200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:49776200-49785200	Weak transcription	Colonic Mucosa	Colon
26	chr3:49776200-49790400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:49776200-49799000	Weak transcription	Fetal Heart	heart
28	chr3:49776200-49802000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:49776400-49784800	Weak transcription	Brain Substantia Nigra	brain
30	chr3:49776400-49784800	Weak transcription	HMEC	breast
31	chr3:49776400-49785000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:49776400-49785000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:49776400-49785200	Weak transcription	Esophagus	oesophagus
34	chr3:49776400-49785200	Weak transcription	Pancreas	Pancrea
35	chr3:49776400-49785200	Weak transcription	Spleen	Spleen
36	chr3:49776400-49785800	Weak transcription	Fetal Lung	lung
37	chr3:49776400-49787400	Weak transcription	Fetal Brain Male	brain
38	chr3:49776400-49788600	Strong transcription	Fetal Thymus	thymus
39	chr3:49776400-49794400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:49776400-49797400	Weak transcription	Small Intestine	intestine
41	chr3:49776400-49812000	Weak transcription	HSMM	muscle
42	chr3:49776400-49812200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:49776400-49812600	Weak transcription	Gastric	stomach
44	chr3:49776400-49818000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:49776400-49818000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:49776400-49818200	Weak transcription	Fetal Kidney	kidney
47	chr3:49776600-49784800	Weak transcription	NHLF	lung
48	chr3:49776600-49785000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:49776600-49785000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:49776600-49785000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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