Variant report

Variant	rs17259208
Chromosome Location	chr2:213316586-213316587
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10168850	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10178687	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10180614	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10194811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10497975	1.00[YRI][hapmap]
rs11675580	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11888697	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11892049	1.00[JPT][hapmap]
rs12987104	0.85[AFR][1000 genomes]
rs13000920	0.85[AFR][1000 genomes]
rs13015808	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs13021394	1.00[JPT][hapmap]
rs13021610	1.00[JPT][hapmap]
rs13389790	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs13430619	0.91[ASN][1000 genomes]
rs1354617	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1384291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1394797	0.89[CHD][hapmap]
rs1505370	1.00[YRI][hapmap]
rs1505371	0.90[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1505372	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1505377	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs16848495	0.89[CHD][hapmap]
rs16848530	1.00[JPT][hapmap]
rs16848550	1.00[JPT][hapmap]
rs16848553	1.00[JPT][hapmap]
rs16848556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16848564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16848571	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs16848593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16848675	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17259910	1.00[YRI][hapmap]
rs17325821	1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs17329875	1.00[JPT][hapmap]
rs1921629	0.85[AFR][1000 genomes]
rs1982717	1.00[YRI][hapmap]
rs2062930	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2062931	0.85[AFR][1000 genomes]
rs2101152	0.91[ASN][1000 genomes]
rs2220024	0.91[ASN][1000 genomes]
rs35610945	0.85[AFR][1000 genomes]
rs55992489	0.95[ASN][1000 genomes]
rs6726147	0.86[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs6735807	1.00[CHB][hapmap]
rs6752299	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73079459	0.95[ASN][1000 genomes]
rs73079470	0.95[ASN][1000 genomes]
rs7569142	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs7575120	0.91[ASN][1000 genomes]
rs9283525	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs979452	1.00[YRI][hapmap]
rs982075	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834527	chr2:213115966-213334308	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1004573	chr2:213186537-213365252	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv875811	chr2:213200920-213347104	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv432024	chr2:213314899-213446726	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17259208	XRCC5	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213312200-213320400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:213314000-213316600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:213314200-213316600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:213315800-213316600	Enhancers	Fetal Heart	heart
5	chr2:213315800-213317200	Enhancers	NHEK	skin
6	chr2:213315800-213317400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:213316200-213316600	Active TSS	A549	lung
8	chr2:213316200-213317000	Enhancers	Fetal Kidney	kidney
9	chr2:213316400-213316600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr2:213316400-213316600	Flanking Active TSS	HepG2	liver
11	chr2:213316400-213316800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:213316400-213316800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:213316400-213316800	Enhancers	Brain Hippocampus Middle	brain
14	chr2:213316400-213317000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr2:213316400-213317000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:213316400-213317000	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:213316400-213317000	Enhancers	Brain Substantia Nigra	brain
18	chr2:213316400-213317000	Enhancers	HMEC	breast
19	chr2:213316400-213317000	Enhancers	HSMMtube	muscle
20	chr2:213316400-213317200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:213316400-213317200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:213316400-213317200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:213316400-213317200	Enhancers	NHDF-Ad	bronchial

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