Variant report

Variant	rs2624819
Chromosome Location	chr3:50010571-50010572
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49977360..49980004-chr3:50009456..50011405,3	K562	blood:

Variant related genes	Relation type
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10049087	0.81[JPT][hapmap]
rs1061474	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1062633	0.82[JPT][hapmap]
rs10865959	0.88[CHB][hapmap]
rs11130222	0.81[ASN][1000 genomes]
rs11130228	0.81[JPT][hapmap]
rs11130233	0.89[JPT][hapmap]
rs1138536	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11706185	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11709503	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11709573	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712056	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11714324	0.85[ASN][1000 genomes]
rs11721204	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107768	0.82[ASN][1000 genomes]
rs12496973	0.82[JPT][hapmap]
rs12634780	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13060128	0.82[JPT][hapmap]
rs13077403	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13079006	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13082703	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1799843	0.89[CHB][hapmap]
rs1799845	0.89[CHB][hapmap]
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]
rs2240329	0.82[JPT][hapmap]
rs2247510	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2252833	0.82[JPT][hapmap]
rs2276864	0.86[CHB][hapmap]
rs2280406	0.82[JPT][hapmap]
rs2352969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2353579	0.82[JPT][hapmap]
rs2526747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526748	0.82[JPT][hapmap]
rs2526749	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526750	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2526751	0.82[JPT][hapmap]
rs2526754	0.82[JPT][hapmap]
rs2624815	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2624821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2624822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2624826	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2624832	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2624834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2624843	0.82[JPT][hapmap]
rs2624847	0.82[JPT][hapmap]
rs2624853	0.82[JPT][hapmap]
rs2681776	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2681778	0.82[AMR][1000 genomes]
rs2681779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
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]
rs2856238	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2883057	0.82[JPT][hapmap]
rs2883059	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34034116	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34312088	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34654589	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35275715	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733134	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs3774734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3774759	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3796386	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4688688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4688689	0.82[JPT][hapmap]
rs4688690	0.82[JPT][hapmap]
rs4688753	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]
rs4688754	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4688755	0.82[JPT][hapmap]
rs4688758	0.82[JPT][hapmap]
rs55692411	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62262114	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446191	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6446192	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6446193	0.82[JPT][hapmap]
rs6446194	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6446195	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6446197	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6762477	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[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];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[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];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6799579	0.82[ASN][1000 genomes]
rs7061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7430334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7613360	0.80[AMR][1000 genomes]
rs7613875	0.82[JPT][hapmap]
rs7615206	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7621026	0.82[JPT][hapmap]
rs7621352	0.82[JPT][hapmap]
rs7626952	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7627864	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7627910	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7628058	0.82[JPT][hapmap]
rs7629936	0.89[CHB][hapmap]
rs7634441	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7648174	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs868891	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311446	0.82[JPT][hapmap]
rs952594	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9682295	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9812936	0.85[EUR][1000 genomes]
rs9814664	0.82[JPT][hapmap]
rs9821675	0.90[JPT][hapmap]
rs9844201	0.83[EUR][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	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
2	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
3	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
4	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2624819	RBM6	cis	Artery Aorta	GTEx
rs2624819	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2624819	RBM6	cis	Nerve Tibial	GTEx
rs2624819	RBM6	cis	Esophagus Mucosa	GTEx
rs2624819	RBM6	cis	Heart Left Ventricle	GTEx
rs2624819	RBM6	cis	Esophagus Muscularis	GTEx
rs2624819	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2624819	RBM6	cis	Artery Tibial	GTEx
rs2624819	RBM6	cis	Thyroid	GTEx
rs2624819	RBM6	cis	Whole Blood	GTEx
rs2624819	RBM6	cis	Adipose Subcutaneous	GTEx
rs2624819	RBM6	cis	lung	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	chr3:49988200-50010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:49992200-50037000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:49995400-50033200	Weak transcription	Fetal Brain Male	brain
5	chr3:49997000-50010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:49997800-50013800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:49998400-50029600	Weak transcription	Fetal Heart	heart
9	chr3:49998400-50078600	Weak transcription	K562	blood
10	chr3:49998800-50019600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:49999800-50011000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:49999800-50028400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:50000000-50019600	Strong transcription	Dnd41	blood
14	chr3:50000600-50011000	Strong transcription	Primary B cells from cord blood	blood
15	chr3:50000600-50011000	Strong transcription	Primary T cells from cord blood	blood
16	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:50003000-50033400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:50003800-50014600	Weak transcription	HSMMtube	muscle
19	chr3:50004200-50016000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:50004400-50010600	Weak transcription	NHDF-Ad	bronchial
21	chr3:50004400-50027600	Weak transcription	NHEK	skin
22	chr3:50004400-50044200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:50004800-50012600	Strong transcription	Fetal Intestine Small	intestine
24	chr3:50005000-50012600	Strong transcription	Fetal Stomach	stomach
25	chr3:50005000-50017400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:50005000-50027600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:50005000-50031400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:50005000-50036800	Weak transcription	Small Intestine	intestine
29	chr3:50005200-50033400	Weak transcription	Esophagus	oesophagus
30	chr3:50005200-50046400	Weak transcription	Psoas Muscle	Psoas
31	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:50005400-50022000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:50005400-50022200	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:50005400-50036800	Weak transcription	Brain Anterior Caudate	brain
35	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
36	chr3:50006200-50012600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:50006200-50014600	Weak transcription	Brain Substantia Nigra	brain
38	chr3:50006200-50027800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:50006200-50028200	Weak transcription	Right Ventricle	heart
40	chr3:50006200-50040800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:50007000-50017600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:50007600-50020000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:50007800-50010600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:50008000-50010600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:50008200-50013800	Weak transcription	Hela-S3	cervix
46	chr3:50008400-50011800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:50008800-50016000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:50009000-50010600	Strong transcription	HSMM	muscle
50	chr3:50009000-50011000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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