Variant report

Variant	rs17653420
Chromosome Location	chr15:38939085-38939086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:38886276..38888617-chr15:38939077..38940605,2	MCF-7	breast:
2	chr15:38878735..38881999-chr15:38938367..38940439,4	MCF-7	breast:
3	chr15:38795646..38798267-chr15:38938759..38941242,2	MCF-7	breast:
4	chr15:38852626..38858205-chr15:38936933..38942203,9	MCF-7	breast:
5	chr15:38925912..38928199-chr15:38938478..38940378,2	MCF-7	breast:
6	chr15:38851398..38858518-chr15:38938422..38942760,10	MCF-7	breast:
7	chr15:38855964..38857124-chr15:38939078..38940526,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172575	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10220877	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16967167	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs17575006	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs17575173	0.84[EUR][1000 genomes]
rs17653702	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2088133	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4318178	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55676440	0.87[ASN][1000 genomes]
rs56094338	0.87[ASN][1000 genomes]
rs56378506	0.87[ASN][1000 genomes]
rs72729347	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72729348	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72729349	0.87[ASN][1000 genomes]
rs72729351	0.93[ASN][1000 genomes]
rs72729355	0.87[ASN][1000 genomes]
rs72729356	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv904085	chr15:38786114-38985513	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38934000-38943400	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr15:38936400-38940000	Weak transcription	Primary B cells from cord blood	blood
3	chr15:38937600-38943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:38937600-38943200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr15:38938200-38941400	Enhancers	Thymus	Thymus
6	chr15:38938400-38941000	Enhancers	Fetal Thymus	thymus
7	chr15:38938400-38942800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr15:38938400-38943200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr15:38938600-38940000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:38938600-38940400	Enhancers	Primary T cells from cord blood	blood
11	chr15:38938600-38941200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:38938600-38941400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr15:38938600-38943000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr15:38938600-38943000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr15:38938800-38939200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:38938800-38939200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr15:38938800-38939200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:38938800-38943000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:38939000-38939200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:38939000-38940000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:38939000-38940200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:38939000-38942600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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