Variant report

Variant	rs1476586
Chromosome Location	chr14:69003504-69003505
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69001801..69004663-chr14:69006865..69008433,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10134446	0.94[JPT][hapmap]
rs1023529	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs11158749	0.88[JPT][hapmap]
rs1859302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040782	0.85[AMR][1000 genomes]
rs2079211	0.92[CHB][hapmap];0.87[AMR][1000 genomes]
rs2107341	0.88[CEU][hapmap];0.90[AMR][1000 genomes]
rs2158358	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2189517	0.88[JPT][hapmap]
rs2244814	0.90[CHB][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap]
rs2247048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525522	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525523	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525524	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842325	0.92[CHB][hapmap];0.85[AMR][1000 genomes]
rs2842329	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2842331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842338	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140266	0.94[JPT][hapmap]
rs757370	0.91[CHB][hapmap];0.87[AMR][1000 genomes]
rs916962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929285	0.92[CHB][hapmap];0.84[AMR][1000 genomes]
rs9323513	0.87[JPT][hapmap]
rs9323514	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1048064	chr14:68991041-69012766	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1476586	ATP6V1D	cis	cerebellum	SCAN
rs1476586	FAM71D	cis	parietal	SCAN
rs1476586	PLEKHG3	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68996200-69007800	Weak transcription	Stomach Mucosa	stomach
2	chr14:69001200-69003600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr14:69001200-69003600	Enhancers	HMEC	breast
4	chr14:69001800-69003600	Enhancers	NHEK	skin
5	chr14:69002000-69003600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr14:69002400-69016600	Weak transcription	Gastric	stomach
7	chr14:69002600-69004800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:69002600-69006600	Weak transcription	Ovary	ovary
9	chr14:69002800-69005600	Weak transcription	A549	lung
10	chr14:69002800-69006000	Weak transcription	Esophagus	oesophagus
11	chr14:69002800-69006000	Weak transcription	Placenta	Placenta
12	chr14:69002800-69006200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr14:69003000-69004800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr14:69003000-69005400	Weak transcription	Fetal Intestine Small	intestine
15	chr14:69003000-69006200	Weak transcription	HSMMtube	muscle
16	chr14:69003000-69006400	Weak transcription	HSMM	muscle
17	chr14:69003000-69007800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr14:69003000-69007800	Weak transcription	Hela-S3	cervix
19	chr14:69003000-69008000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr14:69003000-69009000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr14:69003200-69004800	Weak transcription	Fetal Muscle Leg	muscle
22	chr14:69003200-69005400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr14:69003200-69005800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr14:69003200-69006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr14:69003200-69009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:69003400-69004800	Weak transcription	Psoas Muscle	Psoas
27	chr14:69003400-69006000	Weak transcription	NHDF-Ad	bronchial
28	chr14:69003400-69006000	Weak transcription	NHLF	lung

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