Variant report

Variant	rs11699457
Chromosome Location	chr20:24615239-24615240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24611712..24613428-chr20:24614096..24616788,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11087472	0.94[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11087473	1.00[ASW][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap]
rs11696125	1.00[ASW][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap]
rs11697115	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11697994	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]
rs11699136	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs11699265	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11700002	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	0.92[MEX][hapmap];0.81[TSI][hapmap]
rs13044561	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs34414983	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35378778	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35435987	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35952359	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4140547	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55644719	0.91[EUR][1000 genomes]
rs8126133	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8126153	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv912824	chr20:24612808-24639916	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11699457	XRN2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24608800-24616800	Enhancers	Brain Hippocampus Middle	brain
2	chr20:24610400-24615600	Weak transcription	Right Atrium	heart
3	chr20:24610600-24615600	Weak transcription	Right Ventricle	heart
4	chr20:24610800-24615600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr20:24610800-24615600	Weak transcription	Thymus	Thymus
6	chr20:24611000-24615400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr20:24611400-24615400	Weak transcription	Fetal Thymus	thymus
8	chr20:24613400-24616200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr20:24613400-24616200	Enhancers	HMEC	breast
10	chr20:24613400-24616200	Enhancers	NH-A	brain
11	chr20:24613400-24616600	Enhancers	Brain Substantia Nigra	brain
12	chr20:24613400-24618000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr20:24613600-24615800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:24613600-24616200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:24613800-24616000	Enhancers	Brain Anterior Caudate	brain
16	chr20:24613800-24616000	Enhancers	NHDF-Ad	bronchial
17	chr20:24613800-24616200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr20:24613800-24616200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr20:24613800-24618000	Enhancers	H9 Cell Line	embryonic stem cell
20	chr20:24614000-24615600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr20:24614000-24616000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr20:24614000-24619400	Weak transcription	Gastric	stomach
23	chr20:24614200-24615400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr20:24614200-24615400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:24614200-24619200	Weak transcription	Aorta	Aorta
26	chr20:24614400-24616000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr20:24614400-24616200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr20:24614400-24616600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr20:24614600-24615400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr20:24614600-24615400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr20:24614600-24615400	Weak transcription	Lung	lung
32	chr20:24614600-24615600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr20:24614600-24615600	Weak transcription	Left Ventricle	heart
34	chr20:24614600-24619800	Weak transcription	Esophagus	oesophagus
35	chr20:24614800-24616200	Enhancers	Brain Cingulate Gyrus	brain
36	chr20:24614800-24616400	Enhancers	Brain Angular Gyrus	brain
37	chr20:24614800-24616600	Enhancers	HSMM	muscle
38	chr20:24614800-24617000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr20:24614800-24617800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr20:24614800-24617800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr20:24615000-24615400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr20:24615000-24615600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr20:24615000-24615600	Weak transcription	NHEK	skin
44	chr20:24615000-24616000	Enhancers	Osteobl	bone
45	chr20:24615000-24616200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr20:24615000-24616200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr20:24615000-24616200	Flanking Active TSS	A549	lung
48	chr20:24615000-24616800	Enhancers	HSMMtube	muscle
49	chr20:24615000-24617800	Enhancers	H1 Cell Line	embryonic stem cell
50	chr20:24615200-24615400	Enhancers	Pancreatic Islets	Pancreatic Islet

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