Variant report

Variant	rs490366
Chromosome Location	chr7:26851805-26851806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10228105	0.90[TSI][hapmap]
rs10250097	0.82[CHB][hapmap]
rs10262797	0.85[CHD][hapmap]
rs10277060	1.00[CHB][hapmap]
rs10486480	0.85[CHD][hapmap]
rs1391805	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17323962	0.85[CHD][hapmap]
rs213524	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3801835	0.82[CHB][hapmap]
rs471536	1.00[JPT][hapmap]
rs477924	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs501985	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs534981	1.00[JPT][hapmap]
rs550141	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs558263	0.82[AFR][1000 genomes]
rs564260	1.00[JPT][hapmap]
rs567124	1.00[JPT][hapmap]
rs586947	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs591895	0.83[YRI][hapmap]
rs592359	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622011	1.00[JPT][hapmap]
rs636371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs640512	0.90[YRI][hapmap]
rs668052	0.85[AFR][1000 genomes]
rs673502	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs680704	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs688039	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv887855	chr7:26823963-26872652	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs490366	PRR15	cis	parietal	SCAN
rs490366	HOXA9	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26808000-26854800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:26813000-26871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:26839400-26871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:26843600-26870800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:26843600-26871400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:26843800-26863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:26844400-26853200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:26847200-26853000	Weak transcription	Ovary	ovary
10	chr7:26847400-26853200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:26850000-26869200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:26850200-26853000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:26850200-26861800	Weak transcription	Primary B cells from cord blood	blood
14	chr7:26850200-26862600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr7:26850400-26862600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr7:26850400-26863400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:26850400-26871400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr7:26851600-26852000	Enhancers	Fetal Kidney	kidney
19	chr7:26851800-26852200	Enhancers	Fetal Lung	lung
20	chr7:26851800-26855800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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