Variant report

Variant	rs3010286
Chromosome Location	chr6:139820898-139820899
allele	G/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:18)

rs_ID	r²[population]
rs11155070	0.88[ASN][1000 genomes]
rs1468708	0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[ASN][1000 genomes]
rs1468709	1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs2908512	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2908513	0.84[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3010288	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4896461	0.88[ASN][1000 genomes]
rs4896463	0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6570344	0.84[ASN][1000 genomes]
rs6916887	0.88[ASN][1000 genomes]
rs6923416	0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6926031	0.88[ASN][1000 genomes]
rs9376420	1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[ASN][1000 genomes]
rs9399281	0.85[YRI][hapmap]
rs9399282	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9403080	1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]
rs9403084	0.88[JPT][hapmap];0.81[YRI][hapmap]
rs9495502	0.84[JPT][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1026819	chr6:139813809-139834012	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3010286	IL20RA	cis	cerebellum	SCAN
rs3010286	C6orf115	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139815800-139822800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:139819800-139821200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr6:139819800-139821200	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr6:139820000-139821000	Weak transcription	K562	blood
5	chr6:139820000-139821600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:139820400-139821200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:139820400-139821200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:139820400-139821200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:139820400-139821400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:139820400-139821400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:139820800-139821000	Enhancers	Ovary	ovary
12	chr6:139820800-139821200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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