Variant report

Variant	rs7546586
Chromosome Location	chr1:222168464-222168465
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	chr1:222163800..222166412-chr1:222168403..222170793,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10863672	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863673	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11118913	0.89[ASN][1000 genomes]
rs11118914	0.89[ASN][1000 genomes]
rs11118917	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11118919	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1156668	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12130377	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133266	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339872	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2185326	0.88[JPT][hapmap]
rs2790756	0.89[JPT][hapmap]
rs2790758	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2800856	0.97[ASN][1000 genomes]
rs4475760	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4503353	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6604695	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6671937	0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7546586	RRP15	cis	parietal	SCAN
rs7546586	IARS2	cis	cerebellum	SCAN
rs7546586	USH2A	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222159600-222169400	Enhancers	HMEC	breast
2	chr1:222163600-222169800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:222165000-222171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:222165800-222172000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:222166600-222169400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:222166600-222171800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:222166800-222169200	Enhancers	Osteobl	bone
8	chr1:222167000-222169200	Enhancers	HSMM	muscle
9	chr1:222167000-222169200	Enhancers	NHLF	lung
10	chr1:222167000-222169400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr1:222167000-222172000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:222167200-222168800	Enhancers	GM12878-XiMat	blood
13	chr1:222167200-222169000	Enhancers	HSMMtube	muscle
14	chr1:222167200-222169200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:222167200-222169200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:222167200-222169200	Enhancers	NH-A	brain
17	chr1:222167200-222169400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:222167200-222169400	Enhancers	Brain Anterior Caudate	brain
19	chr1:222167200-222169400	Enhancers	NHDF-Ad	bronchial
20	chr1:222167400-222168600	Enhancers	Brain Hippocampus Middle	brain
21	chr1:222167400-222169000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:222167400-222169200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:222167400-222169200	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:222167600-222168600	Enhancers	Brain Angular Gyrus	brain
25	chr1:222168200-222168600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:222168200-222168600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:222168200-222168600	Weak transcription	Brain Substantia Nigra	brain
28	chr1:222168200-222168600	Weak transcription	NHEK	skin
29	chr1:222168400-222168600	Enhancers	Fetal Lung	lung
30	chr1:222168400-222168800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr1:222168400-222169200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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