Variant report

Variant	rs6082986
Chromosome Location	chr20:23023919-23023920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23021523..23024307-chr20:23024511..23026678,2	MCF-7	breast:
2	chr20:22979981..22982770-chr20:23022858..23025459,2	MCF-7	breast:
3	chr20:23022684..23024263-chr20:23328966..23331361,2	MCF-7	breast:
4	chr20:23023433..23026354-chr20:23029463..23031147,2	K562	blood:

Variant related genes	Relation type
ENSG00000178726	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1042580	0.84[CEU][hapmap]
rs10485639	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13036275	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1331071	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1883956	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2207106	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2207107	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs220990	0.85[CEU][hapmap]
rs2268197	0.81[AFR][1000 genomes]
rs2268199	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2567608	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs2567609	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs34217171	0.86[EUR][1000 genomes]
rs34854430	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34980833	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35745073	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36016048	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3746726	0.96[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3746728	0.83[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6076008	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6076009	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs6076010	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6076012	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6076013	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6082974	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6082975	0.88[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6082977	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6106596	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6113905	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6113908	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6515299	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7262749	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8120756	0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs874585	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912816	chr20:22757960-23062927	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6082986	XRN2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23016000-23026000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:23016200-23028200	Weak transcription	Aorta	Aorta
3	chr20:23017600-23024600	Weak transcription	Spleen	Spleen
4	chr20:23020800-23026400	Weak transcription	A549	lung
5	chr20:23021000-23026800	Weak transcription	HMEC	breast
6	chr20:23021400-23025200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr20:23021600-23026400	Weak transcription	Lung	lung
8	chr20:23021600-23027000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr20:23022200-23024200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
10	chr20:23022400-23024800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr20:23022600-23024000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
12	chr20:23022600-23024000	Enhancers	Brain Germinal Matrix	brain
13	chr20:23022600-23024800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:23022600-23025000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr20:23022800-23024200	Weak transcription	Right Atrium	heart
16	chr20:23023000-23024000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr20:23023000-23024800	Enhancers	Stomach Mucosa	stomach
18	chr20:23023200-23024400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr20:23023400-23024200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr20:23023600-23024000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:23023600-23024000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr20:23023600-23024200	Enhancers	Pancreas	Pancrea
23	chr20:23023600-23024400	Enhancers	Esophagus	oesophagus
24	chr20:23023600-23024800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr20:23023600-23024800	Enhancers	Gastric	stomach
26	chr20:23023800-23024600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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