Variant report

Variant	rs4688753
Chromosome Location	chr3:50074773-50074774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10049087	0.81[JPT][hapmap]
rs1046956	0.82[YRI][hapmap]
rs1061474	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1062633	0.82[JPT][hapmap]
rs10865959	0.88[CHB][hapmap]
rs11130228	0.81[JPT][hapmap]
rs11130233	0.89[JPT][hapmap]
rs1138536	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11706185	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11709503	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11709573	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11712056	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11721204	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12107768	0.98[ASN][1000 genomes]
rs12496973	0.82[JPT][hapmap]
rs12632110	0.83[YRI][hapmap]
rs12634780	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637671	0.83[YRI][hapmap]
rs13060128	0.82[JPT][hapmap]
rs13067082	0.83[YRI][hapmap]
rs13077403	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13079006	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13082703	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1317140	0.89[CHB][hapmap]
rs17657664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17657688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2013208	0.82[JPT][hapmap]
rs2230590	0.82[JPT][hapmap]
rs2240326	0.82[JPT][hapmap]
rs2240327	0.82[JPT][hapmap]
rs2240328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2240329	0.82[JPT][hapmap]
rs2247510	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2252833	0.82[JPT][hapmap]
rs2276864	0.86[CHB][hapmap]
rs2280406	0.82[JPT][hapmap]
rs2352969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2352975	0.90[CHB][hapmap]
rs2352984	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2353579	0.82[JPT][hapmap]
rs2526747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526748	0.82[JPT][hapmap]
rs2526749	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526750	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526751	0.82[JPT][hapmap]
rs2526754	0.82[JPT][hapmap]
rs2624815	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624817	0.95[ASN][1000 genomes]
rs2624819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2624821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2624822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2624826	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2624829	0.83[EUR][1000 genomes]
rs2624832	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2624834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2624843	0.82[JPT][hapmap]
rs2624847	0.82[JPT][hapmap]
rs2624848	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2624853	0.82[JPT][hapmap]
rs2681776	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2681779	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2681780	0.82[JPT][hapmap]
rs2681781	0.82[JPT][hapmap]
rs2777888	0.82[JPT][hapmap]
rs2856237	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856238	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2883057	0.82[JPT][hapmap]
rs2883059	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs34034116	0.80[ASN][1000 genomes]
rs34312088	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35275715	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3733134	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs3774734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3774759	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3796386	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs4688688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4688689	0.82[JPT][hapmap]
rs4688690	0.82[JPT][hapmap]
rs4688754	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688755	0.82[JPT][hapmap]
rs4688758	0.82[JPT][hapmap]
rs62262114	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6446191	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6446192	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6446193	0.82[JPT][hapmap]
rs6446194	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446195	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446197	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6762477	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765484	0.82[JPT][hapmap]
rs6771546	0.82[JPT][hapmap]
rs6772095	0.82[JPT][hapmap]
rs6774354	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6792892	0.82[JPT][hapmap]
rs6793528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799579	0.98[ASN][1000 genomes]
rs6808044	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7430334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613875	0.82[JPT][hapmap]
rs7615206	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7621026	0.82[JPT][hapmap]
rs7621352	0.82[JPT][hapmap]
rs7626952	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7627864	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7627910	0.80[EUR][1000 genomes]
rs7628058	0.82[JPT][hapmap]
rs7634441	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648174	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs868891	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9311446	0.82[JPT][hapmap]
rs952594	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9682295	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812936	0.82[AMR][1000 genomes]
rs9814664	0.82[JPT][hapmap]
rs9821675	0.90[JPT][hapmap]
rs9844201	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9861216	0.82[JPT][hapmap]
rs9866695	0.82[JPT][hapmap]

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	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	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
4	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4688753	RBM6	cis	Esophagus Mucosa	GTEx
rs4688753	RBM6	cis	Thyroid	GTEx
rs4688753	RBM6	cis	Artery Aorta	GTEx
rs4688753	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs4688753	RBM6	cis	Artery Tibial	GTEx
rs4688753	RBM6	cis	Esophagus Muscularis	GTEx
rs4688753	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs4688753	RBM6	cis	Adipose Subcutaneous	GTEx
rs4688753	RBM6	cis	lung	GTEx
rs4688753	RBM6	cis	Heart Left Ventricle	GTEx
rs4688753	RBM6	cis	Nerve Tibial	GTEx
rs4688753	RBM6	cis	Whole Blood	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49998400-50078600	Weak transcription	K562	blood
3	chr3:50010800-50087000	Weak transcription	NHLF	lung
4	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
6	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
8	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
9	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:50039400-50084600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:50041600-50085000	Weak transcription	Fetal Brain Female	brain
15	chr3:50041600-50085400	Weak transcription	Brain Angular Gyrus	brain
16	chr3:50041600-50093400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:50041800-50085200	Weak transcription	Fetal Brain Male	brain
18	chr3:50043400-50085200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:50045200-50085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:50046800-50085800	Weak transcription	HMEC	breast
21	chr3:50047200-50085200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:50047200-50085400	Weak transcription	Left Ventricle	heart
23	chr3:50047200-50092600	Weak transcription	Gastric	stomach
24	chr3:50047400-50085000	Weak transcription	Lung	lung
25	chr3:50048800-50085600	Weak transcription	A549	lung
26	chr3:50049800-50084000	Weak transcription	Brain Germinal Matrix	brain
27	chr3:50051400-50084600	Weak transcription	Spleen	Spleen
28	chr3:50051600-50095200	Weak transcription	Pancreas	Pancrea
29	chr3:50051800-50085000	Weak transcription	Brain Anterior Caudate	brain
30	chr3:50051800-50085400	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:50052200-50084800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:50052200-50087000	Weak transcription	NHDF-Ad	bronchial
33	chr3:50052400-50085600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:50055600-50084200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:50055600-50085600	Weak transcription	Hela-S3	cervix
36	chr3:50056400-50114400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:50056800-50078400	Weak transcription	Ovary	ovary
38	chr3:50057000-50085400	Weak transcription	Fetal Lung	lung
39	chr3:50057200-50085200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:50057200-50085400	Weak transcription	NHEK	skin
41	chr3:50058400-50082600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:50058400-50085600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:50058600-50076400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:50058600-50085200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:50058800-50077400	Weak transcription	HepG2	liver
46	chr3:50058800-50085000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:50058800-50085400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:50059000-50075600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:50059200-50082000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:50059400-50082000	Weak transcription	Rectal Mucosa Donor 31	rectum

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