Variant report

Variant	rs11697994
Chromosome Location	chr20:24600877-24600878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24600299..24601915-chr20:24602393..24603916,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11087472	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11087473	1.00[ASW][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap]
rs11696125	1.00[ASW][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap]
rs11697115	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11699136	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11699265	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11699457	1.00[ASW][hapmap];0.94[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11700002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13041960	0.83[CEU][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs13044561	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34118798	0.84[EUR][1000 genomes]
rs34414983	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35378778	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35435987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35952359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140547	0.83[EUR][1000 genomes]
rs4815285	0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs55644719	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8126133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8126153	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11697994	XRN2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24584400-24612600	Weak transcription	Aorta	Aorta
2	chr20:24591200-24609200	Weak transcription	Brain Anterior Caudate	brain
3	chr20:24594400-24608400	Weak transcription	Spleen	Spleen
4	chr20:24594600-24601200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:24598000-24601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr20:24599800-24601200	Enhancers	Left Ventricle	heart
7	chr20:24600000-24609600	Weak transcription	Brain Angular Gyrus	brain
8	chr20:24600200-24608200	Weak transcription	Brain Hippocampus Middle	brain
9	chr20:24600400-24601200	Enhancers	Fetal Thymus	thymus
10	chr20:24600600-24601400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr20:24600600-24608000	Weak transcription	Right Atrium	heart
12	chr20:24600600-24608400	Weak transcription	Fetal Heart	heart
13	chr20:24600600-24608800	Weak transcription	Thymus	Thymus
14	chr20:24600800-24602000	Weak transcription	Fetal Lung	lung

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