Variant report

Variant	rs4815292
Chromosome Location	chr20:24616186-24616187
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24616131..24617827-chr20:24647064..24649863,2	MCF-7	breast:
2	chr20:24611712..24613428-chr20:24614096..24616788,2	K562	blood:
3	chr20:24610034..24611986-chr20:24615289..24617855,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13040810	0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4813525	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4815293	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6049809	0.92[JPT][hapmap]
rs6083569	0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs6083570	0.80[ASN][1000 genomes]
rs7268328	0.83[ASN][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
rs4815292	XRN2	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24608800-24616800	Enhancers	Brain Hippocampus Middle	brain
2	chr20:24613400-24616200	Enhancers	Muscle Satellite Cultured Cells	--
3	chr20:24613400-24616200	Enhancers	HMEC	breast
4	chr20:24613400-24616200	Enhancers	NH-A	brain
5	chr20:24613400-24616600	Enhancers	Brain Substantia Nigra	brain
6	chr20:24613400-24618000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr20:24613600-24616200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr20:24613800-24616200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr20:24613800-24616200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr20:24613800-24618000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr20:24614000-24619400	Weak transcription	Gastric	stomach
12	chr20:24614200-24619200	Weak transcription	Aorta	Aorta
13	chr20:24614400-24616200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr20:24614400-24616600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr20:24614600-24619800	Weak transcription	Esophagus	oesophagus
16	chr20:24614800-24616200	Enhancers	Brain Cingulate Gyrus	brain
17	chr20:24614800-24616400	Enhancers	Brain Angular Gyrus	brain
18	chr20:24614800-24616600	Enhancers	HSMM	muscle
19	chr20:24614800-24617000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr20:24614800-24617800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr20:24614800-24617800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr20:24615000-24616200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr20:24615000-24616200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr20:24615000-24616200	Flanking Active TSS	A549	lung
25	chr20:24615000-24616800	Enhancers	HSMMtube	muscle
26	chr20:24615000-24617800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr20:24615200-24617000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr20:24615200-24617400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr20:24615200-24617800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr20:24615200-24620200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:24615400-24616200	Enhancers	Fetal Thymus	thymus
32	chr20:24615400-24616200	Enhancers	NHLF	lung
33	chr20:24615400-24617000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr20:24615400-24617400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr20:24615400-24633800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr20:24615600-24619400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr20:24615800-24616200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:24615800-24616600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr20:24615800-24617200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr20:24616000-24616200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr20:24616000-24616200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr20:24616000-24616200	Enhancers	K562	blood
43	chr20:24616000-24616400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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