Variant report

Variant	rs1534542
Chromosome Location	chr15:62362839-62362840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:62357601..62360686-chr15:62360802..62364205,4	MCF-7	breast:
2	chr15:62352114..62355489-chr15:62359291..62363476,4	MCF-7	breast:
3	chr15:62361138..62363897-chr15:62365785..62367372,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259251	Chromatin interaction
ENSG00000129003	Chromatin interaction
ENSG00000198535	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10047986	0.94[ASN][1000 genomes]
rs1030859	0.99[ASN][1000 genomes]
rs1030860	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1030861	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10468026	0.87[ASN][1000 genomes]
rs10468027	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10519153	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10851704	0.83[YRI][hapmap]
rs10851705	0.84[YRI][hapmap]
rs10851707	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071634	0.83[YRI][hapmap]
rs11071647	0.81[CEU][hapmap];0.81[YRI][hapmap]
rs11071650	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11629528	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs11629596	0.96[ASN][1000 genomes]
rs11630347	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11632441	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11632842	0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs11633500	0.85[ASN][1000 genomes]
rs11634516	0.80[YRI][hapmap]
rs11635977	0.98[ASN][1000 genomes]
rs11639147	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11639482	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12438690	0.87[ASN][1000 genomes]
rs12438803	0.94[ASN][1000 genomes]
rs12439356	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs12439934	0.84[YRI][hapmap]
rs12442212	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12442589	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12442675	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12592402	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12592464	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12594658	0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12594946	0.82[ASN][1000 genomes]
rs12898209	0.85[CEU][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12900703	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901575	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12902092	0.80[YRI][hapmap]
rs12912208	0.96[YRI][hapmap]
rs12913951	0.94[ASN][1000 genomes]
rs1344601	0.82[JPT][hapmap]
rs1364810	0.82[CEU][hapmap];0.84[YRI][hapmap]
rs1370177	0.85[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1436958	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1436959	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1436961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436963	0.94[ASN][1000 genomes]
rs1436964	0.94[ASN][1000 genomes]
rs1436965	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1561197	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs17205407	0.94[ASN][1000 genomes]
rs17205463	0.87[ASN][1000 genomes]
rs17271403	0.94[ASN][1000 genomes]
rs17271431	0.80[ASN][1000 genomes]
rs17271438	0.89[ASN][1000 genomes]
rs1836996	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042608	0.81[YRI][hapmap]
rs2042610	0.82[CEU][hapmap]
rs2162062	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2162064	0.87[YRI][hapmap]
rs2414754	0.93[CEU][hapmap]
rs2414759	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28542204	0.99[ASN][1000 genomes]
rs2899677	0.83[ASN][1000 genomes]
rs34096515	0.89[ASN][1000 genomes]
rs34138933	0.83[ASN][1000 genomes]
rs3743294	0.82[CEU][hapmap];0.85[YRI][hapmap]
rs3784445	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3784633	0.84[JPT][hapmap]
rs4143841	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4143842	0.94[ASN][1000 genomes]
rs4143843	0.84[ASN][1000 genomes]
rs4372632	0.89[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4564516	0.99[ASN][1000 genomes]
rs4638519	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4775447	0.80[YRI][hapmap]
rs4775455	0.80[CEU][hapmap];0.87[ASN][1000 genomes]
rs4775457	0.94[ASN][1000 genomes]
rs4775458	0.94[ASN][1000 genomes]
rs7161883	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7162536	0.94[ASN][1000 genomes]
rs7163326	0.83[YRI][hapmap]
rs7164933	0.83[YRI][hapmap]
rs7167876	0.85[AFR][1000 genomes]
rs7168164	0.85[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7177276	0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7177711	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7178424	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7178540	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7178945	0.80[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7182842	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs731820	0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs8025404	0.80[EUR][1000 genomes]
rs8025877	0.80[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs8026008	0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs8032433	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs8038932	0.98[ASN][1000 genomes]
rs8039651	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs893156	0.86[JPT][hapmap]
rs893157	0.89[CEU][hapmap]
rs893158	0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs933807	0.86[JPT][hapmap]
rs9635310	0.89[EUR][1000 genomes]
rs9788670	0.80[YRI][hapmap]
rs9920758	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9989353	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9989354	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking 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	12 gene(s)	inside rSNPs	diseases
2	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers 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	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers 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
5	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1560	chr15:62354264-62399304	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 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	chr15:62361600-62363000	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr15:62361600-62367400	Weak transcription	Hela-S3	cervix

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