Variant report

Variant	rs7542507
Chromosome Location	chr1:224677645-224677646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10495220	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10799573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10799574	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1112556	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121977	0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs12124686	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12128292	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs12140423	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1361618	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2405023	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405028	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3958434	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4517322	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653588	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654045	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56168737	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426129	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6673865	0.85[ASN][1000 genomes]
rs6683524	0.90[ASN][1000 genomes]
rs6688125	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6693653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7531794	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7536124	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536574	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7543421	0.83[AMR][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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7542507	CNIH3	cis	cerebellum	SCAN
rs7542507	FAM177B	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224674800-224677800	Enhancers	H9 Cell Line	embryonic stem cell
2	chr1:224676200-224677800	Enhancers	NHEK	skin
3	chr1:224676400-224677800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr1:224676400-224677800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:224676600-224678000	Enhancers	NHDF-Ad	bronchial
6	chr1:224676800-224677800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:224677000-224677800	Enhancers	HSMMtube	muscle
8	chr1:224677000-224678000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
9	chr1:224677000-224679200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:224677200-224677800	Enhancers	HepG2	liver
11	chr1:224677200-224678200	Enhancers	Osteobl	bone
12	chr1:224677200-224680800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:224677200-224685000	Weak transcription	NHLF	lung
14	chr1:224677400-224678000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:224677400-224678200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr1:224677400-224678200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:224677400-224680400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:224677400-224681000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:224677600-224678400	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:224677600-224678800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:224677600-224680400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:224677600-224682600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:224677600-224683400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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