Variant report

Variant	rs13164720
Chromosome Location	chr5:60602074-60602075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60456737..60461436-chr5:60596585..60603587,8	MCF-7	breast:
2	chr5:60600034..60602668-chr5:60626478..60629464,2	K562	blood:
3	chr5:60599716..60602250-chr5:60620590..60622709,2	MCF-7	breast:
4	chr5:60595162..60604481-chr5:60621758..60631019,20	MCF-7	breast:
5	chr5:60456741..60460015-chr5:60599652..60602524,3	MCF-7	breast:
6	chr5:60600486..60603584-chr5:60608249..60610212,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction
ENSG00000188725	Chromatin interaction
ENSG00000251279	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10939897	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939898	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11743133	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747144	1.00[CEU][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11960587	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs13154581	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs13154663	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156118	0.86[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13162866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13171223	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13174916	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13182603	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4409043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544785	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449526	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs6449527	0.87[CEU][hapmap]
rs6860599	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs6867278	0.88[CEU][hapmap]
rs6870349	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6881622	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6889338	0.88[CEU][hapmap]
rs7704636	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60594000-60602400	Enhancers	NHDF-Ad	bronchial
2	chr5:60594000-60602800	Enhancers	HMEC	breast
3	chr5:60597000-60605000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:60598200-60606600	Weak transcription	Lung	lung
5	chr5:60598600-60602200	Weak transcription	Esophagus	oesophagus
6	chr5:60599400-60603200	Enhancers	Fetal Intestine Large	intestine
7	chr5:60599400-60603400	Enhancers	Placenta	Placenta
8	chr5:60599800-60602200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr5:60599800-60602400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:60600000-60603200	Enhancers	Stomach Mucosa	stomach
11	chr5:60600600-60602200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:60600600-60605200	Enhancers	NHLF	lung
13	chr5:60600600-60609800	Weak transcription	Ovary	ovary
14	chr5:60600800-60602200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr5:60600800-60602400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:60600800-60602400	Enhancers	Osteobl	bone
17	chr5:60600800-60603200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr5:60600800-60615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:60601000-60602200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:60601000-60602200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:60601000-60602200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:60601000-60602200	Weak transcription	HSMMtube	muscle
23	chr5:60601000-60606800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:60601200-60602400	Weak transcription	HSMM	muscle
25	chr5:60601200-60604600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:60601400-60602200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:60601400-60602200	Weak transcription	Fetal Lung	lung
28	chr5:60601400-60602400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr5:60601400-60602400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:60601400-60602800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:60601400-60603800	Enhancers	Hela-S3	cervix
32	chr5:60601400-60604400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:60601600-60602200	Enhancers	A549	lung
34	chr5:60601600-60603400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:60601600-60603800	Enhancers	NHEK	skin
36	chr5:60601800-60602200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:60601800-60602200	Enhancers	GM12878-XiMat	blood
38	chr5:60601800-60602800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:60602000-60602400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:60602000-60603200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:60602000-60603800	Enhancers	Fetal Intestine Small	intestine
42	chr5:60602000-60605000	Enhancers	NH-A	brain

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