Variant report

Variant	rs998144
Chromosome Location	chr6:117488896-117488897
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1405212	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1852292	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693560	0.82[ASN][1000 genomes]
rs509067	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544148	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs560955	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569691	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902977	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6903067	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6903202	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6915129	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7740152	0.92[ASN][1000 genomes]
rs7749803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753558	0.92[ASN][1000 genomes]
rs783362	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961764	0.88[EUR][1000 genomes];0.87[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	nsv948766	chr6:117407275-117641016	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2758076	chr6:117431224-117627275	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2759465	chr6:117431224-117627275	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830785	chr6:117448943-117627275	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2757190	chr6:117464048-117609529	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs998144	RFX6	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117486400-117491200	Enhancers	Fetal Muscle Leg	muscle
2	chr6:117487200-117489600	Enhancers	HSMM	muscle
3	chr6:117487200-117491200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:117487600-117489000	Weak transcription	Left Ventricle	heart
5	chr6:117487600-117489000	Weak transcription	Right Atrium	heart
6	chr6:117487600-117489400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:117487600-117491000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:117488000-117489000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr6:117488000-117489800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:117488000-117490000	Enhancers	Fetal Stomach	stomach
11	chr6:117488000-117491400	Enhancers	NHEK	skin
12	chr6:117488000-117491600	Enhancers	HMEC	breast
13	chr6:117488200-117489000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr6:117488200-117489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:117488200-117491000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:117488400-117489400	Enhancers	HSMMtube	muscle
17	chr6:117488600-117489200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:117488800-117489000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:117488800-117489200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:117488800-117490000	Enhancers	Adipose Nuclei	Adipose
21	chr6:117488800-117490200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:117488800-117490400	Enhancers	Stomach Smooth Muscle	stomach
23	chr6:117488800-117490600	Enhancers	Esophagus	oesophagus
24	chr6:117488800-117490600	Enhancers	Psoas Muscle	Psoas

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