Variant report

Variant	rs538512
Chromosome Location	chr1:179854797-179854798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179853596..179856683-chr1:179859981..179861933,3	MCF-7	breast:
2	chr1:179850478..179853234-chr1:179853885..179855815,2	MCF-7	breast:
3	chr1:179854286..179855981-chr1:179868215..179870330,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264916	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1014394	0.81[EUR][1000 genomes]
rs10913901	0.82[EUR][1000 genomes]
rs1144575	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1148812	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1148815	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12062341	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062383	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281378	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281408	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1281411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1281412	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1281413	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281428	0.93[ASN][1000 genomes]
rs1281429	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281430	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281432	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1298477	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1298479	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1300068	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007148	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245425	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249346	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2762858	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777908	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777909	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777917	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2794582	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2794583	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs474258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475233	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475434	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479094	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480498	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486906	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs501300	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs502036	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs505789	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs505837	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507603	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs514421	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518774	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522534	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530369	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs530854	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs531814	0.82[CEU][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs547776	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549650	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553830	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555526	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs589780	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605807	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609521	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612215	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644412	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv518936	chr1:179847402-179858333	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs538512	MRPS14	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179852800-179858800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:179852800-179859800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:179852800-179860800	Weak transcription	Stomach Mucosa	stomach
4	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
5	chr1:179853000-179855400	Weak transcription	Ovary	ovary
6	chr1:179853000-179857000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:179853000-179858800	Weak transcription	Lung	lung
8	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
9	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:179853200-179854800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:179853200-179855400	Weak transcription	Small Intestine	intestine
12	chr1:179853200-179855800	Enhancers	Rectal Smooth Muscle	rectum
13	chr1:179853200-179857000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:179853200-179857000	Weak transcription	Psoas Muscle	Psoas
15	chr1:179853200-179858800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:179853200-179858800	Weak transcription	Left Ventricle	heart
17	chr1:179853200-179859800	Weak transcription	Colonic Mucosa	Colon
18	chr1:179853200-179859800	Weak transcription	Gastric	stomach
19	chr1:179853200-179859800	Weak transcription	Pancreas	Pancrea
20	chr1:179853200-179861000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:179853400-179854800	Enhancers	Primary hematopoietic stem cells	blood
24	chr1:179853400-179855000	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:179853400-179858800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:179853400-179859000	Weak transcription	HSMMtube	muscle
27	chr1:179853400-179859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
30	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
32	chr1:179853600-179854800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:179853600-179855600	Genic enhancers	Hela-S3	cervix
34	chr1:179853600-179855800	Genic enhancers	Brain Cingulate Gyrus	brain
35	chr1:179853600-179856200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:179853600-179856200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr1:179853600-179858800	Weak transcription	Fetal Kidney	kidney
38	chr1:179853600-179859800	Weak transcription	Aorta	Aorta
39	chr1:179853600-179861600	Strong transcription	Placenta	Placenta
40	chr1:179853800-179855000	Strong transcription	Adipose Nuclei	Adipose
41	chr1:179853800-179855800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:179853800-179855800	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:179853800-179855800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr1:179853800-179855800	Strong transcription	Fetal Thymus	thymus
45	chr1:179853800-179855800	Strong transcription	NHDF-Ad	bronchial
46	chr1:179853800-179856000	Genic enhancers	Primary B cells from cord blood	blood
47	chr1:179853800-179856000	Genic enhancers	Liver	Liver
48	chr1:179853800-179856000	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr1:179853800-179856000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:179853800-179856000	Strong transcription	HMEC	breast

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