Variant report

Variant	rs13232278
Chromosome Location	chr7:83643978-83643979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10239684	0.91[CEU][hapmap]
rs10261519	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10499878	0.86[CEU][hapmap];0.90[GIH][hapmap];0.81[EUR][1000 genomes]
rs11975112	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1357814	0.83[ASW][hapmap];0.85[MEX][hapmap]
rs1404473	0.83[ASW][hapmap];0.84[MEX][hapmap]
rs1404477	0.94[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1404478	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1404480	0.94[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2372022	0.84[MEX][hapmap]
rs2527040	0.82[TSI][hapmap]
rs3801600	0.87[GIH][hapmap]
rs4355720	0.81[MEX][hapmap]
rs6976382	0.86[CEU][hapmap];0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv607707	chr7:83381032-83646816	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv1020784	chr7:83577402-83687108	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv888623	chr7:83596683-83687622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv888624	chr7:83596683-83698177	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv888625	chr7:83616528-83687622	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3352967	chr7:83626144-83684599	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13232278	SLC25A40	cis	parietal	SCAN
rs13232278	ISG15	trans	parietal	SCAN
rs13232278	ZNF500	trans	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83589000-83654600	Weak transcription	Fetal Stomach	stomach
2	chr7:83591200-83654600	Weak transcription	Fetal Muscle Leg	muscle
3	chr7:83606000-83654000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:83609800-83650400	Weak transcription	NHLF	lung
5	chr7:83610200-83673000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:83624400-83651600	Weak transcription	Fetal Intestine Small	intestine
7	chr7:83625000-83646800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:83626000-83650600	Weak transcription	NH-A	brain
9	chr7:83634800-83646200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:83634800-83652000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:83634800-83654600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr7:83635000-83654400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:83635200-83651400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:83635400-83650800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:83636200-83654800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:83636800-83646800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:83638600-83652000	Weak transcription	Colon Smooth Muscle	Colon
18	chr7:83639200-83650600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:83640000-83647000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:83641000-83650600	Weak transcription	NHDF-Ad	bronchial
21	chr7:83642000-83651600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:83642400-83646600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:83642400-83652000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:83643600-83646600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:83643600-83649600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:83643600-83650800	Weak transcription	A549	lung
27	chr7:83643600-83652000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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