Variant report

Variant	rs4688756
Chromosome Location	chr3:50040194-50040195
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1062633	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11130224	0.97[ASN][1000 genomes]
rs11130226	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130228	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130229	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130233	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130234	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713193	0.92[ASN][1000 genomes]
rs11713562	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11925192	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485600	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496973	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13060128	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1317154	0.90[ASN][1000 genomes]
rs2013208	0.83[AMR][1000 genomes]
rs2230590	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2240329	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2245365	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2252833	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280406	0.96[ASN][1000 genomes]
rs2353579	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2353586	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2353587	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526743	0.82[AMR][1000 genomes]
rs2526748	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526751	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2624816	0.82[AMR][1000 genomes]
rs2624823	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2624824	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2624843	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2624844	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2681778	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681780	0.89[ASN][1000 genomes]
rs2681781	0.89[ASN][1000 genomes]
rs2856234	0.81[AMR][1000 genomes]
rs2883057	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34080578	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34831713	0.83[AMR][1000 genomes]
rs35065728	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733135	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3774733	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3774758	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4688689	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688690	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688755	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4688757	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688758	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55751738	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62262093	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6446187	0.92[ASN][1000 genomes]
rs6446189	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6446190	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6446193	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66851636	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6765484	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767381	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6771546	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6772095	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6780731	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792892	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6795703	0.92[ASN][1000 genomes]
rs72942333	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7609971	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7613875	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621026	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621352	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7628058	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7634084	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634917	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7635002	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7650214	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9311446	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9810125	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9814664	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9821433	0.84[ASN][1000 genomes]
rs9821675	0.89[ASN][1000 genomes]
rs9843653	0.90[ASN][1000 genomes]
rs9848497	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9853222	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9856572	0.83[AMR][1000 genomes]
rs9861216	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9862795	0.90[ASN][1000 genomes]
rs9866695	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9881008	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4688756	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs4688756	RBM6	cis	Adipose Subcutaneous	GTEx
rs4688756	RBM6	cis	Stomach	GTEx
rs4688756	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs4688756	RBM6	cis	Heart Left Ventricle	GTEx
rs4688756	RBM6	cis	Esophagus Muscularis	GTEx
rs4688756	RBM6	cis	Thyroid	GTEx
rs4688756	RBM6	cis	lung	GTEx
rs4688756	RBM6	cis	Esophagus Mucosa	GTEx
rs4688756	RBM6	cis	Nerve Tibial	GTEx
rs4688756	RBM6	cis	Whole Blood	GTEx
rs4688756	RBM6	cis	Artery Aorta	GTEx
rs4688756	RBM6	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:49998400-50078600	Weak transcription	K562	blood
4	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:50004400-50044200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:50005200-50046400	Weak transcription	Psoas Muscle	Psoas
7	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
9	chr3:50006200-50040800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:50010800-50087000	Weak transcription	NHLF	lung
12	chr3:50011000-50041000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:50011000-50046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:50011000-50046400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:50011000-50048400	Weak transcription	A549	lung
16	chr3:50011000-50051000	Weak transcription	Pancreas	Pancrea
17	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
19	chr3:50012400-50049000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:50015400-50046400	Weak transcription	Fetal Kidney	kidney
22	chr3:50015800-50041000	Weak transcription	HSMMtube	muscle
23	chr3:50016000-50040800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:50018800-50043600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:50022200-50046400	Weak transcription	Gastric	stomach
26	chr3:50022600-50041200	Weak transcription	Aorta	Aorta
27	chr3:50028000-50056400	Weak transcription	Ovary	ovary
28	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
29	chr3:50029200-50041000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:50029800-50050800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
32	chr3:50031000-50048000	Strong transcription	Fetal Thymus	thymus
33	chr3:50032000-50040200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:50033400-50041400	Strong transcription	Fetal Lung	lung
35	chr3:50033800-50051000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:50035200-50058200	Weak transcription	Esophagus	oesophagus
37	chr3:50035600-50040200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:50035600-50047200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:50036000-50040800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:50036200-50041000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:50036400-50040800	Weak transcription	NHDF-Ad	bronchial
42	chr3:50036400-50041000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:50036400-50046800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:50036600-50040400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
46	chr3:50036800-50041200	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:50036800-50041800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:50036800-50048000	Strong transcription	Fetal Stomach	stomach
49	chr3:50036800-50054600	Strong transcription	Fetal Intestine Small	intestine
50	chr3:50037200-50042800	Strong transcription	Placenta	Placenta

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