Variant report

Variant	rs13032715
Chromosome Location	chr2:40325029-40325030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40322332..40325510-chr2:40329886..40332730,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC8A1-1	chr2:40324916-40328505	NONHSAT070272

Variant related genes	Relation type
ENSG00000227028	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11692733	0.85[ASN][1000 genomes]
rs12151560	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614752	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57918209	0.83[ASN][1000 genomes]
rs6735429	0.81[EUR][1000 genomes]
rs917977	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv962064	chr2:40323393-40328838	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13032715	PLEKHA4	trans	cerebellum	SCAN
rs13032715	HAAO	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40320000-40325600	Enhancers	HSMMtube	muscle
2	chr2:40320000-40325800	Enhancers	NHLF	lung
3	chr2:40320000-40326600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr2:40320000-40332200	Enhancers	HSMM	muscle
5	chr2:40320000-40332600	Enhancers	NHDF-Ad	bronchial
6	chr2:40321000-40326000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:40321200-40326400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:40321200-40327600	Weak transcription	Fetal Intestine Large	intestine
9	chr2:40321200-40354600	Weak transcription	Right Ventricle	heart
10	chr2:40321400-40327000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:40321600-40325200	Enhancers	NHEK	skin
12	chr2:40321800-40325200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:40321800-40325600	Enhancers	HMEC	breast
14	chr2:40322000-40325400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:40322000-40330200	Enhancers	NH-A	brain
16	chr2:40322200-40330200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:40322400-40329600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:40322600-40330200	Weak transcription	Hela-S3	cervix
19	chr2:40322800-40329600	Weak transcription	Fetal Lung	lung
20	chr2:40322800-40350200	Weak transcription	Fetal Brain Male	brain
21	chr2:40323400-40327200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:40323400-40328000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:40323400-40332600	Enhancers	Osteobl	bone
24	chr2:40323600-40330000	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:40323800-40326400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:40324000-40328800	Weak transcription	Ovary	ovary
27	chr2:40324600-40325200	Enhancers	Dnd41	blood
28	chr2:40324600-40326400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:40324800-40325400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:40324800-40329600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:40324800-40330200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:40325000-40325800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:40325000-40326000	Weak transcription	Fetal Heart	heart
34	chr2:40325000-40327400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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