Variant report

Variant	rs515604
Chromosome Location	chr13:54784895-54784896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:54780172..54782257-chr13:54783482..54785302,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1537644	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1832016	0.92[AFR][1000 genomes]
rs2260462	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2261357	0.86[JPT][hapmap]
rs2261359	0.86[JPT][hapmap]
rs2261365	0.86[JPT][hapmap]
rs2576113	0.89[EUR][1000 genomes]
rs2576118	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2576132	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2576143	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2576144	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2576148	0.96[AFR][1000 genomes]
rs2782515	0.89[EUR][1000 genomes]
rs2782517	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2782518	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784552	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2784558	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs484366	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518647	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520026	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538663	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs574751	0.89[EUR][1000 genomes]
rs632059	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636911	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs664745	0.89[EUR][1000 genomes]
rs681748	0.89[EUR][1000 genomes]
rs688466	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs795635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795642	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs795643	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs795652	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs795653	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs795655	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs795656	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs795658	0.96[AFR][1000 genomes]
rs797060	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7993452	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs812128	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3375545	chr13:54517432-54908108	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv561701	chr13:54711276-54826104	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1051063	chr13:54777487-54997866	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv541778	chr13:54777487-54997866	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54782600-54786800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr13:54783200-54785400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr13:54784400-54785400	Enhancers	NHEK	skin
4	chr13:54784400-54785600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr13:54784600-54785000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:54784600-54785000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr13:54784600-54785200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr13:54784600-54785200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr13:54784600-54785200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr13:54784600-54785200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:54784600-54785200	Enhancers	Adipose Nuclei	Adipose
12	chr13:54784600-54785400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr13:54784600-54785400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr13:54784600-54785400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:54784600-54785400	Enhancers	HMEC	breast
16	chr13:54784600-54785600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr13:54784600-54785600	Enhancers	Placenta	Placenta
18	chr13:54784600-54786400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr13:54784800-54785200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:54784800-54785200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr13:54784800-54785400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr13:54784800-54785800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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