Variant report

Variant	rs475377
Chromosome Location	chr15:54009231-54009232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:53489257..53489939-chr15:54008536..54009320,2	MCF-7	breast:
2	chr15:53072398..53073448-chr15:54008592..54010016,9	MCF-7	breast:
3	chr15:53676303..53677625-chr15:54008801..54010344,5	MCF-7	breast:
4	chr15:53072253..53073288-chr15:54008890..54009735,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169856	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10083695	0.87[EUR][1000 genomes]
rs12595408	0.83[EUR][1000 genomes]
rs1316714	0.83[EUR][1000 genomes]
rs1461410	0.83[EUR][1000 genomes]
rs1461411	0.83[EUR][1000 genomes]
rs1585499	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17631603	0.86[EUR][1000 genomes]
rs1982601	0.84[EUR][1000 genomes]
rs2061600	0.83[EUR][1000 genomes]
rs2459379	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2459380	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2470069	0.87[EUR][1000 genomes]
rs2614204	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2614205	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2675336	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474461	0.83[EUR][1000 genomes]
rs4774673	0.87[EUR][1000 genomes]
rs478008	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs551225	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs552960	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs556217	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs578595	0.89[ASN][1000 genomes]
rs6416452	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493640	0.82[EUR][1000 genomes]
rs6493642	0.83[EUR][1000 genomes]
rs689751	0.83[EUR][1000 genomes]
rs690054	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs690214	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs690383	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs690526	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs690625	0.83[EUR][1000 genomes]
rs8037023	0.87[EUR][1000 genomes]
rs8038719	0.88[EUR][1000 genomes];0.90[ASN][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	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv904224	chr15:53668018-54210677	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv9267	chr15:53821005-54132612	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv833010	chr15:53935652-54099849	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1036373	chr15:53993007-54020958	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1048785	chr15:53997956-54020958	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv457146	chr15:54003091-54022123	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv569448	chr15:54003091-54022123	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv569449	chr15:54003104-54013493	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv569450	chr15:54003104-54022123	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs475377	SAMD4A	trans	cerebellum	SCAN
rs475377	GALK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54008800-54009800	Enhancers	A549	lung
2	chr15:54008800-54010000	Enhancers	Liver	Liver
3	chr15:54009200-54014600	Weak transcription	HepG2	liver

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