Variant report

Variant	rs12902997
Chromosome Location	chr15:50427290-50427291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50418543..50420300-chr15:50426585..50429061,2	MCF-7	breast:
2	chr15:50425943..50428562-chr15:50428956..50430506,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10152738	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10519262	0.82[ASN][1000 genomes]
rs11070750	0.99[ASN][1000 genomes]
rs11070751	0.81[ASN][1000 genomes]
rs11070752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11070753	0.91[JPT][hapmap]
rs11631433	0.97[ASN][1000 genomes]
rs11632133	0.81[ASN][1000 genomes]
rs12439182	0.81[ASN][1000 genomes]
rs12442998	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12443171	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12591791	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901981	0.83[ASN][1000 genomes]
rs12915230	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12915287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12915987	0.91[JPT][hapmap]
rs2414025	0.80[ASN][1000 genomes]
rs28403229	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650901	0.96[ASN][1000 genomes]
rs4774556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs5025069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61214575	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7171888	0.91[JPT][hapmap]
rs7177316	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178278	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8023371	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8036777	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037555	0.99[ASN][1000 genomes]
rs933854	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv569395	chr15:50345393-50437494	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12902997	ATP8B4	cis	multi-tissue	Pritchard

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50424200-50429000	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr15:50425200-50429000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:50425800-50428800	Enhancers	Hela-S3	cervix
4	chr15:50425800-50430800	Enhancers	NHDF-Ad	bronchial
5	chr15:50426000-50427600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:50426000-50428800	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:50426000-50429000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:50426000-50429400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:50426000-50430600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:50426000-50430800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:50426400-50427800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:50426400-50427800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:50426400-50427800	Enhancers	HSMMtube	muscle
14	chr15:50426400-50427800	Enhancers	NH-A	brain
15	chr15:50426400-50428000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr15:50426400-50428000	Enhancers	HMEC	breast
17	chr15:50426400-50428000	Enhancers	K562	blood
18	chr15:50426400-50428000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr15:50426400-50428000	Enhancers	NHEK	skin
20	chr15:50426400-50428600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:50426400-50430400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:50426400-50430400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:50426400-50430600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:50426400-50430600	Enhancers	NHLF	lung
25	chr15:50426400-50430800	Enhancers	Osteobl	bone
26	chr15:50426600-50427800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:50426600-50427800	Enhancers	HSMM	muscle
28	chr15:50426600-50428200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr15:50426600-50428200	Flanking Active TSS	A549	lung
30	chr15:50426600-50428400	Enhancers	Colon Smooth Muscle	Colon
31	chr15:50426600-50429000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:50426800-50428000	Enhancers	Primary B cells from cord blood	blood
33	chr15:50426800-50429000	Enhancers	Stomach Smooth Muscle	stomach
34	chr15:50427000-50427400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:50427000-50427800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:50427000-50428800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:50427200-50427400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:50427200-50428400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:50427200-50429800	Weak transcription	HUVEC	blood vessel

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