Variant report

Variant	rs761602
Chromosome Location	chr1:85851308-85851309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17127190	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17127623	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17127637	1.00[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs233075	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs233081	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2389913	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4949902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949903	0.81[EUR][1000 genomes]
rs4949906	0.83[EUR][1000 genomes]
rs553257	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs61769518	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61769519	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61783053	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61783054	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61783058	0.82[EUR][1000 genomes]
rs61785160	0.83[EUR][1000 genomes]
rs7554669	0.84[ASN][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs761602	PKN2	cis	parietal	SCAN
rs761602	C1orf180	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85839800-85864200	Weak transcription	Aorta	Aorta
2	chr1:85841200-85851400	Weak transcription	Pancreas	Pancrea
3	chr1:85841200-85859800	Weak transcription	NH-A	brain
4	chr1:85845000-85852800	Strong transcription	Osteobl	bone
5	chr1:85845000-85870000	Weak transcription	HSMMtube	muscle
6	chr1:85845800-85859800	Weak transcription	NHLF	lung
7	chr1:85846200-85852800	Strong transcription	HSMM	muscle
8	chr1:85848600-85851600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:85849000-85852000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:85849200-85853000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:85849400-85861600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:85849400-85863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:85849600-85852000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:85850000-85851800	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:85850200-85851400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:85850200-85851600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:85850200-85853200	Weak transcription	NHDF-Ad	bronchial
18	chr1:85850200-85853600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:85850200-85854400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:85850400-85851400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:85850400-85852000	Enhancers	Colon Smooth Muscle	Colon
22	chr1:85850800-85853600	Weak transcription	HUVEC	blood vessel
23	chr1:85850800-85853800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:85850800-85863600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:85851000-85851400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:85851000-85853200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:85851000-85853200	Weak transcription	Fetal Lung	lung
28	chr1:85851200-85852000	Weak transcription	Small Intestine	intestine
29	chr1:85851200-85853600	Enhancers	Liver	Liver

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