Variant report

Variant	rs559038
Chromosome Location	chr6:147486764-147486765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1031012	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1031013	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1221645	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1660690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818866	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818868	0.82[EUR][1000 genomes]
rs594981	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs631931	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs652831	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693573	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs694625	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019245	chr6:147350834-147609776	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538467	chr6:147350834-147609776	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886751	chr6:147354092-147490398	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv886752	chr6:147443480-147729477	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147478400-147487600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:147478400-147487600	Weak transcription	HMEC	breast
3	chr6:147478400-147487600	Weak transcription	NHLF	lung
4	chr6:147483000-147491000	Weak transcription	NH-A	brain
5	chr6:147483400-147487600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:147483800-147487200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:147483800-147487600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:147483800-147487600	Weak transcription	Osteobl	bone
9	chr6:147483800-147487800	Weak transcription	NHEK	skin
10	chr6:147484200-147487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:147485400-147488800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:147486000-147491200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:147486200-147486800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:147486600-147486800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr6:147486600-147486800	Transcr. at gene 5' and 3'	K562	blood
16	chr6:147486600-147487000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:147486600-147488400	Enhancers	HUVEC	blood vessel

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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