Variant report

Variant	rs490634
Chromosome Location	chr3:50640830-50640831
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50624498..50626370-chr3:50639043..50642026,2	K562	blood:
2	chr3:50626963..50632967-chr3:50633102..50640850,17	K562	blood:
3	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
4	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088543	Chromatin interaction
ENSG00000114735	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1034405	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130252	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130255	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11710858	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs11719998	0.82[EUR][1000 genomes]
rs12491425	0.83[EUR][1000 genomes]
rs12639126	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs129310	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs13075377	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13076850	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13083004	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13084476	0.89[EUR][1000 genomes]
rs13084771	0.81[ASN][1000 genomes]
rs13091933	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs13094336	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13094785	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes]
rs13095920	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13096264	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13096772	0.83[CEU][hapmap];0.81[ASN][1000 genomes]
rs1458386	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1458387	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1463496	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1463497	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs175634	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17787569	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1824280	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1824281	0.84[CEU][hapmap]
rs201193	0.87[EUR][1000 genomes]
rs201194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201196	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs201197	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs201198	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2125366	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2125369	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2168866	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2199050	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2227280	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2232248	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs2232253	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2262810	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2269505	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs2269507	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2355321	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2355323	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs2608988	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2609001	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2609006	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2609024	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2609036	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2675772	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2675773	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2675806	0.83[CEU][hapmap]
rs2675810	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2675812	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2675816	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2883652	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34202063	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34267788	0.85[EUR][1000 genomes]
rs34399912	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34434811	0.85[EUR][1000 genomes]
rs34584636	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34632971	0.81[ASN][1000 genomes]
rs34756253	0.89[EUR][1000 genomes]
rs34846525	0.81[ASN][1000 genomes]
rs34889917	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35655236	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35690191	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35714264	0.90[EUR][1000 genomes]
rs35864641	0.85[EUR][1000 genomes]
rs375544	0.83[CEU][hapmap]
rs3792325	0.84[CEU][hapmap]
rs3792328	0.83[CEU][hapmap]
rs3804627	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs3804628	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs391620	0.82[EUR][1000 genomes]
rs3943212	0.84[CEU][hapmap]
rs396302	0.83[CEU][hapmap]
rs398703	0.83[EUR][1000 genomes]
rs399484	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs399971	0.85[EUR][1000 genomes]
rs414171	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs417592	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs441516	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs4429624	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs443030	0.86[EUR][1000 genomes]
rs443436	0.84[CEU][hapmap]
rs448028	0.84[CEU][hapmap]
rs4482663	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4533647	0.85[EUR][1000 genomes]
rs453570	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs4688702	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59949730	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs616589	0.84[CEU][hapmap]
rs622502	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs628081	0.89[CEU][hapmap]
rs6446212	0.83[CEU][hapmap]
rs6446213	0.83[CEU][hapmap]
rs6446214	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66867590	0.81[ASN][1000 genomes]
rs67425923	0.81[EUR][1000 genomes]
rs67588094	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6768300	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6775012	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6776224	0.82[CEU][hapmap]
rs6778680	0.83[CEU][hapmap]
rs6779819	0.83[CEU][hapmap]
rs67813889	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6784166	0.90[EUR][1000 genomes]
rs6787521	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6791880	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6796769	0.83[CEU][hapmap]
rs695170	0.87[EUR][1000 genomes]
rs71326937	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs728901	0.84[CEU][hapmap]
rs73082948	0.83[EUR][1000 genomes]
rs750453	0.82[EUR][1000 genomes]
rs750510	0.84[CEU][hapmap]
rs7611428	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7615703	0.83[CEU][hapmap]
rs7629253	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7646236	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs7650574	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7652715	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs809451	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs809454	0.83[EUR][1000 genomes]
rs813243	0.83[CEU][hapmap]
rs900735	0.84[CEU][hapmap]
rs936405	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs936406	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9682401	0.84[CEU][hapmap]
rs9826757	0.82[CEU][hapmap]
rs9830920	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9838283	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9839684	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs490634		cis	Lymphoblastoid	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50636000-50641200	Enhancers	Lung	lung
2	chr3:50636000-50641400	Enhancers	Fetal Thymus	thymus
3	chr3:50636000-50641600	Enhancers	Esophagus	oesophagus
4	chr3:50636400-50641000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:50636400-50641600	Enhancers	Pancreas	Pancrea
6	chr3:50636600-50643600	Enhancers	Left Ventricle	heart
7	chr3:50636800-50641600	Enhancers	Gastric	stomach
8	chr3:50636800-50646000	Genic enhancers	Fetal Intestine Small	intestine
9	chr3:50637600-50641200	Enhancers	Small Intestine	intestine
10	chr3:50638000-50641200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:50638600-50641000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:50638800-50647400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:50639000-50642400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:50639000-50643600	Weak transcription	Aorta	Aorta
15	chr3:50639000-50643800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:50639000-50648000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:50639200-50642200	Enhancers	Stomach Mucosa	stomach
18	chr3:50639400-50641400	Enhancers	Liver	Liver
19	chr3:50639400-50641400	Enhancers	Right Ventricle	heart
20	chr3:50639400-50641600	Enhancers	Adipose Nuclei	Adipose
21	chr3:50639400-50642200	Weak transcription	GM12878-XiMat	blood
22	chr3:50639400-50648000	Weak transcription	Fetal Brain Female	brain
23	chr3:50639600-50642800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:50639600-50646800	Genic enhancers	Spleen	Spleen
25	chr3:50639600-50648000	Weak transcription	Fetal Brain Male	brain
26	chr3:50639800-50641400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr3:50639800-50641600	Enhancers	Colonic Mucosa	Colon
28	chr3:50639800-50641800	Enhancers	K562	blood
29	chr3:50639800-50642800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr3:50639800-50644200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:50639800-50644800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:50639800-50648000	Weak transcription	HUVEC	blood vessel
33	chr3:50639800-50648200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:50639800-50648200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:50639800-50648200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:50640000-50641400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr3:50640000-50641800	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr3:50640000-50642200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:50640000-50642200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:50640000-50643200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr3:50640000-50644200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:50640000-50644600	Weak transcription	Thymus	Thymus
43	chr3:50640000-50647000	Genic enhancers	Fetal Muscle Leg	muscle
44	chr3:50640000-50648000	Weak transcription	Brain Substantia Nigra	brain
45	chr3:50640000-50648200	Weak transcription	NH-A	brain
46	chr3:50640200-50641200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:50640200-50641200	Weak transcription	Psoas Muscle	Psoas
48	chr3:50640200-50641600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:50640200-50641800	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr3:50640200-50642000	Weak transcription	Primary B cells from peripheral blood	blood

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