Variant report

Variant	rs10220855
Chromosome Location	chr15:54894502-54894503
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11632253	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11632366	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11852668	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11852743	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12592900	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12592914	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12708436	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1356857	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1520411	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1818704	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1818711	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1850994	0.92[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1851000	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs1851005	0.86[CEU][hapmap]
rs1851010	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1972137	0.92[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2414327	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2414331	0.80[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2414332	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2460605	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2460606	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2553216	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2553217	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2553220	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2553221	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs2553225	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2681958	0.81[ASN][1000 genomes]
rs2681959	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2911846	0.82[EUR][1000 genomes]
rs2911847	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2947001	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs3848141	0.92[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3959676	0.81[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493694	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6493695	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9284299	0.87[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1038660	chr15:54756184-55039913	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv904236	chr15:54820897-54912439	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1039548	chr15:54856965-54914519	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv569508	chr15:54876212-54904782	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv526413	chr15:54876423-54904782	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv904237	chr15:54888537-54927484	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv569509	chr15:54888537-54932716	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv457154	chr15:54892583-54904782	Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv569517	chr15:54892583-54904782	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10220855	XPC	cis	Cerebellum	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54893800-54894600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:54893800-54895400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr15:54894200-54894600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr15:54894400-54894600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:54894400-54895200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:54894400-54895200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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