Variant report

Variant	rs3096604
Chromosome Location	chr8:95628254-95628255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1866844	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2304765	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2890827	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3096600	0.96[ASN][1000 genomes]
rs3098705	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3098711	0.85[CHB][hapmap]
rs3098721	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3098724	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs3099418	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3099420	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3099425	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3102860	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3133646	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3133659	0.90[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv429928	chr8:95488800-95672033	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv429929	chr8:95564533-95676894	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv516679	chr8:95616980-95638496	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3096604	TSPYL5	cis	parietal	SCAN
rs3096604	DPY19L4	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95625600-95635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:95626400-95632400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr8:95628000-95628600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr8:95628000-95628600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr8:95628000-95628800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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Input of quick search could be:

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

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