Variant report

Variant	rs12438604
Chromosome Location	chr15:32972997-32972998
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	chr15:32962834..32965663-chr15:32971694..32973378,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241818	Chromatin interaction
ENSG00000166922	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12102176	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441136	0.82[CHB][hapmap]
rs12441140	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.99[ASN][1000 genomes]
rs12442397	0.83[CHB][hapmap]
rs28688414	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3817592	0.83[CHB][hapmap]
rs6494587	0.90[YRI][hapmap]
rs7177176	0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs7177843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178316	0.90[YRI][hapmap]
rs8024160	0.90[YRI][hapmap]
rs8043234	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431374	chr15:32008985-32976055	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv469587	chr15:32821940-32986579	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv482780	chr15:32821940-32986579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv482680	chr15:32958401-33154005	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv568915	chr15:32965357-32994056	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv456787	chr15:32968923-33023951	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv568916	chr15:32968923-33023951	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12438604	CHRNA7	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:32956200-32973800	Weak transcription	HSMM	muscle
2	chr15:32961200-32976200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:32961200-32980200	Weak transcription	Thymus	Thymus
4	chr15:32963000-32974200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:32964600-32990800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:32964800-32993800	Weak transcription	Fetal Brain Male	brain
7	chr15:32965000-32974000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:32965000-32983600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:32968800-32974000	Weak transcription	NHEK	skin
10	chr15:32968800-32974200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:32968800-32974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr15:32969800-32974000	Weak transcription	Brain Angular Gyrus	brain
13	chr15:32970000-32974000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:32970000-32974000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:32970000-32974000	Weak transcription	Osteobl	bone
16	chr15:32970000-32974400	Weak transcription	Brain Anterior Caudate	brain
17	chr15:32970000-32974400	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:32970000-32974400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:32970000-32974400	Weak transcription	Hela-S3	cervix
20	chr15:32970000-32977800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:32970000-32982600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:32970200-32973800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:32970200-32974000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:32970200-32974000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:32970200-32974000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:32970200-32974000	Weak transcription	NH-A	brain
27	chr15:32970200-32974400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:32970200-32974400	Weak transcription	Brain Substantia Nigra	brain
29	chr15:32970200-32974600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:32970200-32976200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:32970200-32977800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:32970200-32979400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:32970200-32979600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:32971200-32974200	Weak transcription	Adipose Nuclei	Adipose
35	chr15:32972000-32973800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:32972000-32973800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:32972000-32974000	Weak transcription	NHDF-Ad	bronchial
38	chr15:32972000-32979400	Weak transcription	HepG2	liver
39	chr15:32972200-32973400	Enhancers	Liver	Liver
40	chr15:32972200-32974200	Weak transcription	A549	lung
41	chr15:32972200-32974600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:32972200-32974600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr15:32972600-32975600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr15:32972800-32973200	Strong transcription	Brain Germinal Matrix	brain
45	chr15:32972800-32976600	Strong transcription	Fetal Brain Female	brain

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