Variant report

Variant	rs9495639
Chromosome Location	chr6:140428456-140428457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13362768	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6570389	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6902659	1.00[ASW][hapmap];0.84[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6937739	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7746257	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7746402	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7747450	0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7748387	1.00[AMR][1000 genomes]
rs7750737	1.00[AMR][1000 genomes]
rs7762281	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7774903	1.00[AMR][1000 genomes]
rs9484341	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484344	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484345	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484346	1.00[AMR][1000 genomes]
rs9484350	1.00[ASW][hapmap];0.84[LWK][hapmap]
rs9495643	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9495665	1.00[AMR][1000 genomes]
rs9885887	0.87[AFR][1000 genomes];1.00[AMR][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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr6:140426400-140428600	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr6:140426400-140428800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr6:140426800-140431000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:140426800-140431000	Weak transcription	Brain Germinal Matrix	brain
5	chr6:140426800-140431000	Weak transcription	Fetal Brain Female	brain
6	chr6:140427400-140431000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:140427400-140436000	Weak transcription	Placenta	Placenta
8	chr6:140428000-140428800	Enhancers	NHEK	skin
9	chr6:140428200-140428600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:140428200-140428600	Enhancers	Rectal Smooth Muscle	rectum
11	chr6:140428200-140428800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:140428200-140428800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:140428200-140429000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:140428200-140429800	Enhancers	Fetal Heart	heart
15	chr6:140428400-140428600	Enhancers	Colon Smooth Muscle	Colon
16	chr6:140428400-140430800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:140428400-140430800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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