Variant report

Variant	rs12903325
Chromosome Location	chr15:50353277-50353278
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50331487..50333450-chr15:50352450..50354634,2	K562	blood:
2	chr15:50346066..50347875-chr15:50350812..50353705,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10519257	0.85[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs12050709	0.95[CEU][hapmap];0.95[CHB][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12902530	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12905011	0.87[EUR][1000 genomes]
rs12909131	0.84[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs28369108	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34970637	0.85[EUR][1000 genomes]
rs41362650	0.90[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493402	0.86[GIH][hapmap]
rs7172615	0.90[CEU][hapmap];0.94[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7177318	0.86[GIH][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12903325	ATP8B4	cis	multi-tissue	Pritchard
rs12903325	ATP8B4	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50344200-50356600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr15:50348200-50359800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:50348600-50358600	Weak transcription	Fetal Intestine Large	intestine
4	chr15:50350000-50353400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr15:50350800-50353400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr15:50350800-50354600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:50351000-50358400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:50351400-50353400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:50351600-50353400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr15:50351600-50354200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:50351800-50353400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr15:50352000-50358400	Weak transcription	Fetal Intestine Small	intestine
13	chr15:50352000-50358600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:50352000-50358600	Weak transcription	Small Intestine	intestine
15	chr15:50352200-50357000	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:50352400-50359400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:50352600-50354000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:50352600-50354600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:50352600-50356400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:50353000-50353800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:50353200-50353600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr15:50353200-50354200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr15:50353200-50355400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr15:50353200-50356800	Weak transcription	Gastric	stomach
25	chr15:50353200-50357800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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