Variant report

Variant	rs175254
Chromosome Location	chr20:15181590-15181591
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs149820	0.90[CHD][hapmap]
rs175223	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs175258	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs175259	0.93[CHD][hapmap];0.83[GIH][hapmap]
rs175260	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs175262	0.87[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap]
rs175265	0.90[CHD][hapmap]
rs175266	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs175269	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs175277	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175278	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175283	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175293	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs175298	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs175305	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6105373	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6110544	0.82[LWK][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]

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	nsv1065152	chr20:14781684-15305258	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv912767	chr20:14854935-15189598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv585540	chr20:14858910-15242365	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1066220	chr20:14883338-15204628	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv868936	chr20:14928568-15183054	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1063917	chr20:14939608-15206129	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv912778	chr20:14949763-15207464	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1062252	chr20:14964258-15547739	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv544206	chr20:14964258-15547739	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv932106	chr20:14964459-15203333	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv524481	chr20:15007730-15382919	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv916795	chr20:15041479-15345528	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv1062960	chr20:15045757-15204628	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1057455	chr20:15069821-15198608	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
15	nsv1060275	chr20:15084485-15327541	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv526767	chr20:15086277-15223632	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv1058827	chr20:15159151-15289719	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv1066112	chr20:15165512-15206129	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15180000-15181600	Enhancers	GM12878-XiMat	blood
2	chr20:15180000-15186600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

Quick Search:

Input of quick search could be:

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

what's new

Quick links