Variant report

Variant	rs13417558
Chromosome Location	chr2:46881613-46881614
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46878154..46881998-chr2:46882962..46887664,5	K562	blood:
2	chr2:46873644..46875189-chr2:46880714..46882765,2	MCF-7	breast:
3	chr2:46879813..46881998-chr2:46882962..46885478,2	K562	blood:
4	chr2:46880745..46883271-chr2:46889135..46890937,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10495934	0.81[CEU][hapmap];0.92[CHD][hapmap];0.80[MEX][hapmap];0.85[EUR][1000 genomes]
rs10495935	0.81[JPT][hapmap]
rs13013245	0.81[JPT][hapmap]
rs13024534	0.84[ASN][1000 genomes]
rs13406427	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035488	0.81[JPT][hapmap]
rs17035489	0.83[JPT][hapmap]
rs17767994	0.84[ASN][1000 genomes]
rs17768018	0.84[ASN][1000 genomes]
rs17768132	0.84[ASN][1000 genomes]
rs17768138	0.84[ASN][1000 genomes]
rs17768226	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17819022	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2122715	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs34449783	0.84[ASN][1000 genomes]
rs34748737	0.84[ASN][1000 genomes]
rs34996358	0.82[ASN][1000 genomes]
rs35449212	0.82[ASN][1000 genomes]
rs35837037	0.84[ASN][1000 genomes]
rs35949012	0.84[ASN][1000 genomes]
rs4952837	0.84[ASN][1000 genomes]
rs55742873	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62136873	0.84[ASN][1000 genomes]
rs62136894	0.84[ASN][1000 genomes]
rs62136895	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62136898	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544909	0.80[EUR][1000 genomes]
rs6746598	0.84[ASN][1000 genomes]
rs7605089	1.00[ASN][1000 genomes]
rs896212	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
7	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13417558	ATP6V1E2	cis	multi-tissue	Pritchard
rs13417558	CRIPT	cis	multi-tissue	Pritchard
rs13417558	SOCS5	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46869400-46883400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:46869800-46882200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:46870000-46891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:46870200-46889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:46872000-46883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:46873400-46881800	Weak transcription	Brain Angular Gyrus	brain
7	chr2:46873400-46883400	Weak transcription	Right Ventricle	heart
8	chr2:46873400-46884000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:46874600-46883600	Weak transcription	Placenta	Placenta
10	chr2:46877600-46883400	Weak transcription	Spleen	Spleen
11	chr2:46877600-46884400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:46878400-46884600	Enhancers	NHLF	lung
13	chr2:46879200-46883400	Weak transcription	Adipose Nuclei	Adipose
14	chr2:46879200-46883400	Weak transcription	HSMM	muscle
15	chr2:46879400-46883400	Weak transcription	Ovary	ovary
16	chr2:46879400-46884600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:46879600-46882200	Weak transcription	NHDF-Ad	bronchial
18	chr2:46879800-46882200	Weak transcription	A549	lung
19	chr2:46879800-46884800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:46880000-46883400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:46880000-46884800	Enhancers	Osteobl	bone
22	chr2:46880400-46883800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:46880600-46883400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:46880600-46884600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:46880800-46884800	Enhancers	Fetal Lung	lung
26	chr2:46881200-46882800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:46881200-46882800	Weak transcription	HSMMtube	muscle
28	chr2:46881400-46882400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:46881400-46883400	Weak transcription	Lung	lung
30	chr2:46881600-46882600	Weak transcription	NH-A	brain
31	chr2:46881600-46883400	Weak transcription	Right Atrium	heart

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