Variant report

Variant	rs6702162
Chromosome Location	chr1:94275467-94275468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1004197	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11165012	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165016	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125652	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2179908	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391313	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4075343	0.99[EUR][1000 genomes]
rs6541396	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6661992	0.95[EUR][1000 genomes]
rs6662311	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679619	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6687914	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6692717	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515462	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521365	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536914	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7537445	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7547179	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7552104	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9729722	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546822	chr1:94246577-94289863	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1815663	chr1:94246577-94291252	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1877	chr1:94247756-94292908	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv508415	chr1:94256122-94305339	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1802380	chr1:94272119-94291252	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6702162	GCLM	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94271000-94279200	Weak transcription	Adipose Nuclei	Adipose
2	chr1:94271200-94275800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:94271200-94276000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:94271200-94276000	Weak transcription	Placenta	Placenta
5	chr1:94271200-94276000	Weak transcription	Right Atrium	heart
6	chr1:94271200-94276000	Weak transcription	Right Ventricle	heart
7	chr1:94271200-94276600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:94271200-94276600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:94271200-94278200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:94272000-94276000	Weak transcription	HSMM	muscle
11	chr1:94272000-94276000	Weak transcription	NHLF	lung
12	chr1:94273400-94275800	Weak transcription	Hela-S3	cervix
13	chr1:94273600-94276000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:94273600-94278600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:94273600-94282800	Weak transcription	Lung	lung
16	chr1:94274200-94278200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:94274400-94275800	Weak transcription	HMEC	breast
18	chr1:94274600-94276000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:94274800-94276200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:94274800-94279400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:94275400-94279600	Enhancers	NHDF-Ad	bronchial
22	chr1:94275400-94280200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:94275400-94281400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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