Variant report

Variant	rs12187752
Chromosome Location	chr5:59073172-59073173
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10043265	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs10043283	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs1027747	0.96[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10514857	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs11949859	0.81[ASN][1000 genomes]
rs12188131	0.85[ASN][1000 genomes]
rs13155799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13168347	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1362941	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs1362942	0.85[ASN][1000 genomes]
rs1437124	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1504982	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504984	0.93[ASN][1000 genomes]
rs16877195	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs17369708	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs17381667	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs17381695	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs17382202	0.83[CHB][hapmap];0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs17440909	0.83[CHB][hapmap]
rs17441217	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs17441825	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs17742120	0.83[CHB][hapmap];0.80[CHD][hapmap];0.83[ASN][1000 genomes]
rs17742544	0.83[CHB][hapmap];0.80[CHD][hapmap];0.85[ASN][1000 genomes]
rs17743216	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs17799161	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs2164660	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs28583502	0.90[ASN][1000 genomes]
rs2938780	0.96[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2938783	0.86[GIH][hapmap];0.80[TSI][hapmap]
rs2963826	0.96[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs298063	0.80[TSI][hapmap]
rs298084	0.80[TSI][hapmap]
rs298091	0.82[TSI][hapmap]
rs36143327	0.91[EUR][1000 genomes]
rs3898713	0.83[CHB][hapmap];0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs4577665	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699943	0.83[CHB][hapmap];0.91[ASN][1000 genomes]
rs4700340	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs4700341	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs4700342	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55704150	0.90[ASN][1000 genomes]
rs55868825	0.85[ASN][1000 genomes]
rs56199003	0.85[ASN][1000 genomes]
rs6450528	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs6450530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6860907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6874708	0.93[ASN][1000 genomes]
rs6889294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897073	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs72751211	0.81[ASN][1000 genomes]
rs72751218	0.81[ASN][1000 genomes]
rs72751226	0.83[ASN][1000 genomes]
rs72751229	0.85[ASN][1000 genomes]
rs72751231	0.85[ASN][1000 genomes]
rs72751232	0.85[ASN][1000 genomes]
rs72751233	0.85[ASN][1000 genomes]
rs72751234	0.85[ASN][1000 genomes]
rs72751235	0.85[ASN][1000 genomes]
rs72751237	0.85[ASN][1000 genomes]
rs72751241	0.85[ASN][1000 genomes]
rs72751244	0.85[ASN][1000 genomes]
rs72751247	0.85[ASN][1000 genomes]
rs72751250	0.85[ASN][1000 genomes]
rs72751252	0.88[ASN][1000 genomes]
rs72751264	0.91[ASN][1000 genomes]
rs756211	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs756212	0.83[CHB][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs7708952	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7710199	0.93[ASN][1000 genomes]
rs7736817	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs877745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs981230	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59066000-59081200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:59068200-59085800	Weak transcription	Primary B cells from cord blood	blood
3	chr5:59069200-59081400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:59070000-59081400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:59072200-59073400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:59072200-59081200	Weak transcription	A549	lung
7	chr5:59072400-59073200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:59072400-59073400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr5:59072400-59073400	Enhancers	Colon Smooth Muscle	Colon
10	chr5:59072400-59073800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:59072600-59073200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:59072800-59073200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:59072800-59073200	Enhancers	Aorta	Aorta
14	chr5:59072800-59073400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
15	chr5:59073000-59073400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:59073000-59073400	Enhancers	Brain Cingulate Gyrus	brain
17	chr5:59073000-59073400	Enhancers	Brain Germinal Matrix	brain
18	chr5:59073000-59073400	Enhancers	Rectal Smooth Muscle	rectum

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