Variant report

Variant	rs10117271
Chromosome Location	chr9:9482268-9482269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10119835	0.85[JPT][hapmap]
rs10491614	0.91[JPT][hapmap]
rs10759074	0.89[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap]
rs10759075	0.95[JPT][hapmap]
rs10759076	0.80[JPT][hapmap]
rs10759079	0.82[JPT][hapmap]
rs10816128	0.95[JPT][hapmap]
rs10816129	0.85[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs10816133	0.90[JPT][hapmap]
rs10816135	0.85[JPT][hapmap]
rs10816141	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs10816142	0.85[JPT][hapmap]
rs10977764	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs10977778	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs10977783	0.89[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap]
rs1120438	0.95[JPT][hapmap]
rs11531684	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs12686617	0.90[JPT][hapmap]
rs1332192	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1332194	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1332195	0.89[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1332196	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1332210	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs1332212	0.80[JPT][hapmap]
rs1332213	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs1332807	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs1333107	0.92[CEU][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap]
rs1333108	0.91[JPT][hapmap]
rs1333114	0.91[JPT][hapmap]
rs1412871	0.86[JPT][hapmap]
rs1412872	0.92[CEU][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs1467790	0.91[JPT][hapmap]
rs1576794	0.81[CEU][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1576797	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1576798	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs16929560	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs17831559	0.85[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2026984	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2382014	0.85[JPT][hapmap]
rs2382015	0.85[JPT][hapmap]
rs2382018	0.81[JPT][hapmap]
rs4237177	0.85[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4388502	0.85[JPT][hapmap]
rs4451355	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs4484751	0.92[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4742602	0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs4742603	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7027963	0.85[JPT][hapmap]
rs7044905	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7465855	0.88[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap]
rs7468723	0.91[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap]
rs867979	0.87[ASN][1000 genomes]
rs944641	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs955474	0.89[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs987353	0.84[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498066	chr9:8961722-9486652	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1025791	chr9:9294304-9626331	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1016302	chr9:9355676-9549587	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv539982	chr9:9355676-9549587	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv613308	chr9:9409606-9750139	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1033808	chr9:9431799-9777960	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv528425	chr9:9437674-9556992	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv892264	chr9:9440838-9796577	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1034257	chr9:9444744-9526138	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
10	nsv1016118	chr9:9444744-9582169	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1034584	chr9:9458137-9486282	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
12	nsv892265	chr9:9476425-9796116	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1020932	chr9:9481247-9534062	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10117271	PDCD1LG2	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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