Variant report

Variant	rs7713247
Chromosome Location	chr5:178219977-178219978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:178219935..178220578-chr5:178266097..178266710,3	MCF-7	breast:
2	chr5:178211735..178215494-chr5:178218190..178221753,4	MCF-7	breast:
3	chr5:178219910..178220433-chr5:178257274..178257901,2	MCF-7	breast:
4	chr5:178219922..178220838-chr5:178920668..178921270,2	MCF-7	breast:
5	chr5:178219952..178220766-chr5:178688074..178688887,3	MCF-7	breast:
6	chr5:178219826..178220832-chr5:178266011..178266987,10	MCF-7	breast:
7	chr5:178157501..178158373-chr5:178219857..178220443,3	MCF-7	breast:
8	chr5:178219841..178220793-chr5:178920740..178921735,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11249573	0.85[GIH][hapmap]
rs11952919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956290	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957056	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655252	0.86[ASN][1000 genomes]
rs12658342	0.96[ASN][1000 genomes]
rs13174784	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs34180938	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701068	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61469010	0.95[ASN][1000 genomes]
rs6600954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600955	0.91[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6600956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6600957	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6874045	0.96[ASN][1000 genomes]
rs73324174	0.81[ASN][1000 genomes]
rs73341509	0.95[ASN][1000 genomes]
rs73341510	0.93[ASN][1000 genomes]
rs73341513	0.96[ASN][1000 genomes]
rs73341521	0.96[ASN][1000 genomes]
rs73341529	0.96[ASN][1000 genomes]
rs73341553	0.86[ASN][1000 genomes]
rs7444422	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs7447672	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711944	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720287	0.95[ASN][1000 genomes]
rs7722026	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs7725396	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs7733056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031206	chr5:178149292-178283614	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537973	chr5:178149292-178283614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv462573	chr5:178180299-178241495	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv600452	chr5:178180299-178241495	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv12687	chr5:178218220-178220656	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7713247	C5orf25	cis	parietal	SCAN
rs7713247	RNF44	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178166600-178224000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:178218000-178220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:178218000-178220400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:178218000-178220800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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