Variant report

Variant	rs11700002
Chromosome Location	chr20:24591936-24591937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11087472	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][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];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11697994	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]
rs11699136	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11699265	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][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];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11699457	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13041960	0.83[CEU][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs13044561	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34118798	0.85[EUR][1000 genomes]
rs34414983	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35378778	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35435987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35952359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4140547	0.82[EUR][1000 genomes]
rs55644719	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8126133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8126153	0.94[AMR][1000 genomes];0.97[EUR][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
rs11700002	XRN2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24583200-24599800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr20:24584400-24612600	Weak transcription	Aorta	Aorta
3	chr20:24589400-24594000	Weak transcription	Primary T cells from cord blood	blood
4	chr20:24590000-24592200	Enhancers	Brain Cingulate Gyrus	brain
5	chr20:24590000-24592400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr20:24590000-24592600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:24590200-24592000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr20:24590400-24592000	Enhancers	NH-A	brain
9	chr20:24590400-24592400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:24590400-24592600	Enhancers	HMEC	breast
11	chr20:24590800-24592000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr20:24590800-24592400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr20:24591000-24592000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:24591000-24592200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr20:24591000-24592400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr20:24591200-24592000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr20:24591200-24592000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr20:24591200-24609200	Weak transcription	Brain Anterior Caudate	brain
19	chr20:24591400-24592000	Enhancers	Dnd41	blood
20	chr20:24591400-24592200	Enhancers	NHEK	skin
21	chr20:24591400-24592400	Enhancers	Thymus	Thymus
22	chr20:24591600-24593400	Weak transcription	Brain Substantia Nigra	brain
23	chr20:24591600-24597600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr20:24591800-24592000	Enhancers	Brain Hippocampus Middle	brain

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