Variant report

Variant	rs10063808
Chromosome Location	chr5:2087916-2087917
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:2086623..2089378-chr5:2750285..2752647,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170561	Chromatin interaction
ENSG00000186493	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10039186	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10039370	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10039392	0.85[AFR][1000 genomes]
rs10041106	0.83[EUR][1000 genomes]
rs10043989	0.83[EUR][1000 genomes]
rs10056211	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10060649	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10062782	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10066240	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10066385	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10066597	0.83[AFR][1000 genomes]
rs10067919	0.83[AFR][1000 genomes]
rs10068233	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10068847	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10069051	0.94[EUR][1000 genomes]
rs10069104	0.94[EUR][1000 genomes]
rs10070853	0.83[EUR][1000 genomes]
rs10073733	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10075502	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10428571	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11741616	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11741646	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13354874	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13355387	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13357993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13357995	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13358051	0.85[EUR][1000 genomes]
rs13358958	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13359444	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13360716	0.83[EUR][1000 genomes]
rs13362263	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28702040	0.94[EUR][1000 genomes]
rs57862430	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61659441	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62327939	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62329475	0.82[EUR][1000 genomes]
rs62329476	0.83[EUR][1000 genomes]
rs73732562	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1032759	chr5:2044117-2091631	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1020211	chr5:2045699-2104887	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv523478	chr5:2075162-2091155	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10063808	SDHA	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:2087200-2088200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:2087200-2088200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr5:2087400-2088400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:2087600-2088000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:2087600-2088400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:2087800-2088000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:2087800-2088200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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