Variant report

Variant	rs2840795
Chromosome Location	chr6:73575403-73575404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12526205	0.82[AFR][1000 genomes]
rs12664704	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs17800259	0.84[MKK][hapmap]
rs1891396	0.87[GIH][hapmap];0.86[LWK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs1891398	0.83[AFR][1000 genomes]
rs2796005	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2840797	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2995346	0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs3005764	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3005769	0.87[GIH][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs3763159	0.87[GIH][hapmap]
rs6930157	0.87[MKK][hapmap]
rs9342981	0.88[YRI][hapmap]
rs9351950	0.87[GIH][hapmap]
rs9351951	0.87[GIH][hapmap];0.86[LWK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs9360608	0.88[YRI][hapmap]
rs9360610	0.82[MKK][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	nsv830691	chr6:73530978-73743648	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv470834	chr6:73546750-73596605	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
3	nsv886155	chr6:73551937-73649330	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2840795	KCNQ5	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73569600-73575600	Enhancers	HSMMtube	muscle
2	chr6:73570400-73576600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr6:73571000-73576200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:73572000-73590200	Weak transcription	GM12878-XiMat	blood
5	chr6:73572200-73576400	Enhancers	HSMM	muscle
6	chr6:73572400-73576000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:73572600-73583800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:73573800-73576000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:73574000-73576000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:73574200-73576000	Weak transcription	Psoas Muscle	Psoas
11	chr6:73574600-73576000	Enhancers	HMEC	breast
12	chr6:73574800-73575600	Enhancers	Liver	Liver
13	chr6:73574800-73575800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:73574800-73575800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:73574800-73575800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr6:73574800-73576000	Enhancers	NHEK	skin
17	chr6:73575000-73576000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr6:73575000-73576200	Weak transcription	Aorta	Aorta
19	chr6:73575200-73575600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:73575200-73575600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr6:73575200-73575800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:73575200-73575800	Enhancers	NHDF-Ad	bronchial
23	chr6:73575200-73576000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:73575400-73575600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:73575400-73575600	Enhancers	NHLF	lung
26	chr6:73575400-73575800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:73575400-73576000	Enhancers	Osteobl	bone

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