Variant report

Variant	rs10084347
Chromosome Location	chr2:72780746-72780747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10165868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10176180	0.85[AFR][1000 genomes]
rs10179254	1.00[MEX][hapmap]
rs10181491	0.84[AFR][1000 genomes]
rs10188321	0.81[AFR][1000 genomes]
rs10188854	0.85[AFR][1000 genomes]
rs10191381	1.00[YRI][hapmap]
rs10206245	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13385811	1.00[MEX][hapmap]
rs13391821	1.00[MEX][hapmap]
rs13393356	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs13397728	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap]
rs13397743	1.00[MEX][hapmap]
rs13411428	0.84[YRI][hapmap]
rs13414789	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13415635	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13419598	1.00[MEX][hapmap]
rs13426691	0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs13431249	0.84[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs28860196	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs590345	0.92[YRI][hapmap]
rs6715775	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6729155	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749568	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9653555	0.80[AFR][1000 genomes]

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	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1008335	chr2:72561463-72819704	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv582208	chr2:72690622-72835886	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv834257	chr2:72701083-72853548	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10084347	PRRX1	trans	lymphoblastoid	seeQTL
rs10084347	DSC3	trans	lymphoblastoid	seeQTL
rs10084347	IL1R2	trans	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72761400-72783000	Weak transcription	Aorta	Aorta
2	chr2:72766400-72782800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:72766600-72786400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:72766800-72781400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:72766800-72788000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:72766800-72788600	Weak transcription	NH-A	brain
7	chr2:72766800-72789200	Weak transcription	NHEK	skin
8	chr2:72768800-72786800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:72774000-72783000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:72775000-72808800	Weak transcription	Ovary	ovary
11	chr2:72776600-72783000	Weak transcription	Fetal Lung	lung
12	chr2:72776800-72783000	Weak transcription	Brain Substantia Nigra	brain
13	chr2:72777200-72781400	Weak transcription	HUVEC	blood vessel
14	chr2:72777200-72789000	Weak transcription	Brain Angular Gyrus	brain
15	chr2:72779000-72783200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:72779600-72783000	Weak transcription	A549	lung
17	chr2:72780200-72781000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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