Variant report

Variant	rs2974516
Chromosome Location	chr5:114448597-114448598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114447493..114449912-chr5:114504036..114505819,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152503	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10039629	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs10055823	0.85[ASN][1000 genomes]
rs10061081	0.83[ASN][1000 genomes]
rs10061288	0.83[ASN][1000 genomes]
rs10077885	0.85[ASN][1000 genomes]
rs10078015	0.85[ASN][1000 genomes]
rs10477526	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs11241305	0.83[ASN][1000 genomes]
rs13360458	0.88[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs1446074	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1838747	0.92[ASN][1000 genomes]
rs2121188	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2921618	0.96[ASN][1000 genomes]
rs2921625	0.96[ASN][1000 genomes]
rs2921626	0.95[ASN][1000 genomes]
rs2921629	0.94[ASN][1000 genomes]
rs2974505	0.93[ASN][1000 genomes]
rs2974506	0.96[ASN][1000 genomes]
rs2974507	0.96[ASN][1000 genomes]
rs2974609	0.80[ASN][1000 genomes]
rs2974610	0.96[ASN][1000 genomes]
rs2974612	0.96[ASN][1000 genomes]
rs4073838	0.83[ASN][1000 genomes]
rs4073839	0.83[ASN][1000 genomes]
rs4075509	0.83[ASN][1000 genomes]
rs4075510	0.82[ASN][1000 genomes]
rs4076057	0.83[ASN][1000 genomes]
rs4131436	0.81[ASN][1000 genomes]
rs4131437	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4235764	0.83[ASN][1000 genomes]
rs4235765	0.83[ASN][1000 genomes]
rs4235768	0.83[ASN][1000 genomes]
rs4235769	0.85[ASN][1000 genomes]
rs4235770	0.85[ASN][1000 genomes]
rs4286654	0.81[ASN][1000 genomes]
rs4312873	0.83[ASN][1000 genomes]
rs4360034	0.85[ASN][1000 genomes]
rs4382158	0.83[ASN][1000 genomes]
rs4392610	0.83[ASN][1000 genomes]
rs4421095	0.85[ASN][1000 genomes]
rs4435857	0.89[ASN][1000 genomes]
rs4485921	0.84[ASN][1000 genomes]
rs4485922	0.83[ASN][1000 genomes]
rs4489055	0.85[ASN][1000 genomes]
rs4554207	0.83[ASN][1000 genomes]
rs4705720	0.89[ASN][1000 genomes]
rs6878888	0.89[ASN][1000 genomes]
rs7722841	0.83[ASN][1000 genomes]
rs966791	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882729	chr5:113743628-114497708	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv830453	chr5:114277261-114546536	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv462398	chr5:114445023-114475774	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv599476	chr5:114445023-114475774	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv462399	chr5:114445023-114526010	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv599477	chr5:114445023-114526010	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2974516	TSSK1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114445800-114449200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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