Variant report

Variant	rs16892042
Chromosome Location	chr6:81347875-81347876
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11751136	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11755775	0.83[AMR][1000 genomes]
rs11757148	0.83[AMR][1000 genomes]
rs11760053	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1454458	0.82[AMR][1000 genomes]
rs16892048	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16892086	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs16892116	0.82[AMR][1000 genomes]
rs55741904	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59534131	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73479784	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73479786	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531333	chr6:81042427-81836484	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1019670	chr6:81086504-81569984	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv915714	chr6:81134888-81366749	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1020533	chr6:81288890-81406533	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv538340	chr6:81288890-81406533	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv604085	chr6:81297890-81439973	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1015520	chr6:81309213-81374699	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv886314	chr6:81341175-81379791	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16892042	CA12	trans	brain	seeQTL
rs16892042	HTR4	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:81333000-81348200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:81346200-81349400	Enhancers	Osteobl	bone
3	chr6:81346200-81349600	Enhancers	NHLF	lung
4	chr6:81346400-81349200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:81346400-81349200	Enhancers	NHDF-Ad	bronchial
6	chr6:81346800-81350600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:81347000-81348000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:81347000-81348200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:81347000-81348200	Weak transcription	HSMM	muscle
10	chr6:81347200-81348000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:81347200-81348600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:81347200-81349400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr6:81347400-81348800	Enhancers	A549	lung
14	chr6:81347400-81349400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:81347600-81348800	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr6:81347800-81348200	Enhancers	HUVEC	blood vessel
17	chr6:81347800-81349000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:81347800-81349200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:81347800-81349200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr6:81347800-81349200	Enhancers	HMEC	breast
21	chr6:81347800-81349400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr6:81347800-81349400	Enhancers	NH-A	brain
23	chr6:81347800-81349800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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