Variant report

Variant	rs7760148
Chromosome Location	chr6:140201675-140201676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17069435	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17069437	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4896495	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs590585	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs613274	0.85[JPT][hapmap]
rs618471	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs642162	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs660269	0.93[ASN][1000 genomes]
rs6904492	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs7744208	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs856648	0.84[ASN][1000 genomes]
rs856649	0.91[ASN][1000 genomes]
rs9376477	1.00[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9376478	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9389730	0.81[JPT][hapmap]
rs9484321	0.81[JPT][hapmap]

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	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	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7760148	IL22RA2	cis	cerebellum	SCAN
rs7760148	MAP3K5	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140190800-140203400	Weak transcription	Fetal Lung	lung
2	chr6:140191600-140203000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:140194400-140203000	Weak transcription	NHLF	lung
4	chr6:140194800-140204200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:140199400-140202400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:140199400-140202600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:140201000-140206400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:140201200-140202200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:140201200-140202400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:140201200-140203000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:140201200-140203200	Weak transcription	Placenta	Placenta
12	chr6:140201400-140202600	Weak transcription	Osteobl	bone
13	chr6:140201400-140203000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:140201400-140203000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:140201400-140203400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:140201400-140204200	Weak transcription	Liver	Liver
17	chr6:140201600-140202000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:140201600-140203000	Weak transcription	K562	blood

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

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