Variant report

Variant	rs2624816
Chromosome Location	chr3:50117312-50117313
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10049087	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130233	0.81[ASN][1000 genomes]
rs11130234	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11713562	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11925192	0.82[AMR][1000 genomes]
rs12485600	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13060128	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2008877	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2013208	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071206	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2071207	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240326	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240327	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240329	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245365	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301166	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2353579	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2353586	0.82[AMR][1000 genomes]
rs2353587	0.83[AMR][1000 genomes]
rs2526743	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526748	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526751	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526754	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624823	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2624824	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2624825	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2624847	0.83[ASN][1000 genomes]
rs2624853	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2856234	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2856236	0.85[EUR][1000 genomes]
rs34080578	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34831713	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733133	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3774733	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4688686	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4688689	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4688690	0.81[ASN][1000 genomes]
rs4688755	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688756	0.82[AMR][1000 genomes]
rs4688757	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4688758	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6446193	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs66851636	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6765484	0.85[AMR][1000 genomes]
rs6767381	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6780731	0.81[ASN][1000 genomes]
rs7428430	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621352	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7628058	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7642934	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7650214	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9311446	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9810125	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814664	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9853222	0.81[ASN][1000 genomes]
rs9856572	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861216	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9866695	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers 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	24 gene(s)	inside rSNPs	diseases
5	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
6	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv822079	chr3:50116177-50126157	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2624816	RBM6	cis	lung	GTEx
rs2624816	RBM6	cis	Adipose Subcutaneous	GTEx
rs2624816	RBM6	cis	Artery Aorta	GTEx
rs2624816	RBM6	cis	Nerve Tibial	GTEx
rs2624816	RBM6	cis	Artery Tibial	GTEx
rs2624816	RBM6	cis	Stomach	GTEx
rs2624816	RBM6	cis	Heart Left Ventricle	GTEx
rs2624816	RBM6	cis	Esophagus Muscularis	GTEx
rs2624816	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2624816	RBM6	cis	Whole Blood	GTEx
rs2624816	RBM6	cis	Esophagus Mucosa	GTEx
rs2624816	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2624816	RBM6	cis	Thyroid	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50104200-50123400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:50106200-50125800	Weak transcription	Stomach Mucosa	stomach
3	chr3:50108800-50126000	Weak transcription	Fetal Heart	heart
4	chr3:50110200-50126000	Weak transcription	NHLF	lung
5	chr3:50110600-50125800	Weak transcription	Small Intestine	intestine
6	chr3:50111000-50125800	Weak transcription	Colonic Mucosa	Colon
7	chr3:50111000-50126000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:50111200-50119000	Weak transcription	Fetal Brain Male	brain
9	chr3:50111200-50119800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:50111200-50126200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:50112200-50125800	Weak transcription	K562	blood
12	chr3:50112800-50119600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:50113000-50119400	Weak transcription	Esophagus	oesophagus
14	chr3:50113000-50125800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:50113000-50125800	Weak transcription	A549	lung
16	chr3:50113000-50126000	Weak transcription	NH-A	brain
17	chr3:50113200-50119600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:50113200-50119600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:50113200-50119600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:50113200-50119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:50113200-50119600	Weak transcription	HUVEC	blood vessel
22	chr3:50113200-50120200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:50113200-50120200	Weak transcription	Spleen	Spleen
24	chr3:50113200-50125600	Weak transcription	HepG2	liver
25	chr3:50113200-50125800	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:50113200-50125800	Weak transcription	Gastric	stomach
27	chr3:50113200-50125800	Weak transcription	Pancreas	Pancrea
28	chr3:50113200-50125800	Weak transcription	Psoas Muscle	Psoas
29	chr3:50113200-50126200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:50113400-50117800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:50113400-50118000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:50113400-50118800	Weak transcription	Primary B cells from cord blood	blood
33	chr3:50113400-50118800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:50113400-50119600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:50113400-50125600	Weak transcription	Dnd41	blood
36	chr3:50113400-50125800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:50113400-50125800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:50113400-50125800	Weak transcription	Brain Substantia Nigra	brain
39	chr3:50113400-50125800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:50113400-50125800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:50113400-50125800	Weak transcription	Hela-S3	cervix
42	chr3:50113400-50125800	Weak transcription	HMEC	breast
43	chr3:50113400-50125800	Weak transcription	NHEK	skin
44	chr3:50113400-50126000	Weak transcription	Fetal Kidney	kidney
45	chr3:50113400-50126000	Weak transcription	Fetal Lung	lung
46	chr3:50113400-50126000	Weak transcription	HSMMtube	muscle
47	chr3:50113600-50119600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:50114600-50119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:50114600-50126000	Weak transcription	Ovary	ovary
50	chr3:50114800-50117400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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