Variant report

Variant	rs4253993
Chromosome Location	chr10:1580662-1580663
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10751803	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10794754	0.83[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10794755	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs10794756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[ASN][1000 genomes]
rs10794757	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10903472	0.83[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10903473	0.87[ASN][1000 genomes]
rs10903477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs10903478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs10903479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10903481	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs11250593	0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11250594	0.86[ASN][1000 genomes]
rs11250596	0.87[ASN][1000 genomes]
rs11250597	0.86[ASN][1000 genomes]
rs11250600	0.87[ASN][1000 genomes]
rs11250607	0.82[ASN][1000 genomes]
rs11250608	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs11250609	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs11250610	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs11250613	0.82[ASN][1000 genomes]
rs11250614	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11250615	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11250616	0.82[ASN][1000 genomes]
rs11250623	0.84[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs12220558	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12220566	0.92[ASN][1000 genomes]
rs12244289	0.83[ASN][1000 genomes]
rs12412937	0.82[ASN][1000 genomes]
rs17221818	0.81[CHB][hapmap]
rs2138691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2138692	0.83[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2676732	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2676733	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2676776	0.92[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2676778	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2813449	0.83[JPT][hapmap];0.80[MEX][hapmap]
rs2813451	0.83[JPT][hapmap];0.85[MEX][hapmap]
rs2813453	0.93[ASN][1000 genomes]
rs2813454	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2813458	0.94[ASN][1000 genomes]
rs2813460	0.91[ASN][1000 genomes]
rs2813461	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2813462	0.87[CHB][hapmap]
rs2944604	0.88[EUR][1000 genomes]
rs34032124	0.86[ASN][1000 genomes]
rs4376829	0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4440958	0.84[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap]
rs4880858	0.89[JPT][hapmap]
rs4880864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4880867	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs61831943	0.82[ASN][1000 genomes]
rs7079988	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7080610	0.82[ASN][1000 genomes]
rs7082956	0.93[ASN][1000 genomes]
rs7095474	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7099162	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7903267	0.87[ASN][1000 genomes]
rs7914665	0.84[CEU][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1041498	chr10:1117200-1760190	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1052682	chr10:1162925-1675641	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1043944	chr10:1168095-1626019	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv540411	chr10:1168095-1626019	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1046041	chr10:1195214-2189155	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1037054	chr10:1232041-1865296	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv540413	chr10:1232041-1865296	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv549769	chr10:1244020-1764966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv549786	chr10:1293100-1904598	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv894736	chr10:1513349-1672408	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1054555	chr10:1558145-1965145	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv894737	chr10:1560338-1692796	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv1814319	chr10:1580035-1585629	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv1801488	chr10:1580235-1585463	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv1809254	chr10:1580235-1585463	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv1826381	chr10:1580235-1585463	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4253993	PITRM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1577400-1580800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:1580200-1581200	Strong transcription	Dnd41	blood
3	chr10:1580400-1581800	Enhancers	Fetal Thymus	thymus

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