Variant report

Variant	rs11740396
Chromosome Location	chr5:178082841-178082842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178082180..178084775-chr5:178097053..178099400,3	MCF-7	breast:
2	chr5:178068917..178070441-chr5:178081330..178082973,2	MCF-7	breast:
3	chr5:178072351..178074150-chr5:178081295..178082959,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10051137	0.82[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs10061455	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10061883	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10064009	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10070794	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10073925	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs10479501	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11742564	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11744815	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11953546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12654185	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12654187	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12719855	0.84[CHB][hapmap]
rs13360296	0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs1472457	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs1967419	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs262028	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs4073633	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4077796	0.82[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap]
rs4079109	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4079111	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4079112	0.93[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4301240	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4413550	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4418123	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4437394	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4521498	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60509476	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6600942	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6866952	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs6869889	0.82[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs6871074	0.85[EUR][1000 genomes]
rs6874126	0.95[EUR][1000 genomes]
rs6881073	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs721143	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs73353860	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73353883	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs752043	0.81[JPT][hapmap]
rs7707891	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs776153	0.88[CHB][hapmap];0.82[JPT][hapmap]

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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	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
3	nsv1023697	chr5:178070594-178126328	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv537972	chr5:178070594-178126328	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv5155	chr5:178075100-178132799	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3381395	chr5:178082246-178086544	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178082000-178083000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:178082200-178083000	Enhancers	Fetal Heart	heart
3	chr5:178082400-178083000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr5:178082400-178083000	Enhancers	H9 Cell Line	embryonic stem cell
5	chr5:178082400-178083000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:178082400-178083000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:178082400-178083000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:178082400-178083000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:178082400-178083000	Enhancers	NHDF-Ad	bronchial
10	chr5:178082600-178083000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:178082600-178083000	Flanking Active TSS	Rectal Smooth Muscle	rectum
12	chr5:178082600-178083000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
13	chr5:178082600-178083000	Flanking Active TSS	Osteobl	bone

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