Variant report

Variant	rs4540297
Chromosome Location	chr6:82723807-82723808
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10755418	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10943842	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12194197	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12199519	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1361686	0.81[TSI][hapmap]
rs1418296	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1418299	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1418300	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1418301	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1935417	0.92[EUR][1000 genomes]
rs1935418	0.92[EUR][1000 genomes]
rs4449673	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4535596	0.92[EUR][1000 genomes]
rs4706917	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6903637	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6913193	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6937709	0.81[TSI][hapmap]

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	nsv1020783	chr6:82720632-82732325	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1021793	chr6:82720632-82737456	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1034389	chr6:82721569-82746599	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4540297	FAM46A	cis	cerebellum	SCAN
rs4540297	SH3BGRL2	cis	cerebellum	SCAN
rs4540297	HMGN3	cis	parietal	SCAN
rs4540297	TBX18	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:82716000-82724400	Weak transcription	Right Atrium	heart
2	chr6:82721600-82727600	Enhancers	HUVEC	blood vessel
3	chr6:82721800-82724200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:82722400-82724800	Enhancers	NHDF-Ad	bronchial
5	chr6:82722400-82728200	Enhancers	Hela-S3	cervix
6	chr6:82722600-82725400	Enhancers	Aorta	Aorta
7	chr6:82722800-82724000	Enhancers	Liver	Liver
8	chr6:82722800-82727600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:82722800-82728000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:82723000-82724800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:82723000-82727800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:82723000-82728400	Enhancers	HMEC	breast
13	chr6:82723200-82725400	Enhancers	NH-A	brain
14	chr6:82723200-82725800	Enhancers	NHEK	skin
15	chr6:82723200-82726200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:82723400-82724000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:82723400-82725200	Enhancers	NHLF	lung
18	chr6:82723400-82725800	Enhancers	Osteobl	bone
19	chr6:82723600-82724200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:82723600-82725000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:82723600-82725600	Enhancers	Ovary	ovary
22	chr6:82723600-82726400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:82723600-82727800	Enhancers	HSMM	muscle
24	chr6:82723800-82724000	Enhancers	HSMMtube	muscle
25	chr6:82723800-82724200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:82723800-82724200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:82723800-82724600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:82723800-82725000	Weak transcription	HepG2	liver
29	chr6:82723800-82726600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:82723800-82727000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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