Variant report

Variant	rs10939897
Chromosome Location	chr5:60600524-60600525
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:60586340..60593423-chr5:60595007..60600646,11	MCF-7	breast:
2	chr5:60596613..60601643-chr5:60625817..60629986,6	MCF-7	breast:
3	chr5:60456737..60461436-chr5:60596585..60603587,8	MCF-7	breast:
4	chr5:60474350..60475293-chr5:60600116..60600975,7	MCF-7	breast:
5	chr5:60600034..60602668-chr5:60626478..60629464,2	K562	blood:
6	chr5:60599716..60602250-chr5:60620590..60622709,2	MCF-7	breast:
7	chr5:60600075..60600721-chr5:60916464..60917476,4	MCF-7	breast:
8	chr5:60595162..60604481-chr5:60621758..60631019,20	MCF-7	breast:
9	chr5:60600516..60602032-chr5:60603241..60605744,2	MCF-7	breast:
10	chr5:60600204..60601079-chr5:60916454..60917327,5	MCF-7	breast:
11	chr5:60600075..60601015-chr5:60916464..60917512,9	MCF-7	breast:
12	chr5:60474401..60475293-chr5:60600199..60600951,3	MCF-7	breast:
13	chr5:60576541..60577260-chr5:60600117..60600681,2	MCF-7	breast:
14	chr5:60456741..60460015-chr5:60599652..60602524,3	MCF-7	breast:
15	chr5:60464543..60465310-chr5:60600109..60601074,3	MCF-7	breast:
16	chr5:60600486..60603584-chr5:60608249..60610212,3	MCF-7	breast:

No data

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

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10939898	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11743133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11747144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11960587	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs13154581	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs13154663	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13156118	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13162866	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13164720	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]
rs13171223	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13174916	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13178686	0.91[CEU][hapmap]
rs13182603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4409043	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4513641	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4544785	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62366236	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449525	0.81[EUR][1000 genomes]
rs6449526	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6449527	0.84[CEU][hapmap]
rs6860599	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6867278	0.84[CEU][hapmap]
rs6870349	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6881622	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6889338	0.84[CEU][hapmap]
rs7704636	0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60594000-60602400	Enhancers	NHDF-Ad	bronchial
2	chr5:60594000-60602800	Enhancers	HMEC	breast
3	chr5:60596800-60601800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:60597000-60605000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:60598000-60600600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:60598000-60600600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:60598000-60601200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:60598200-60600600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:60598200-60601000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:60598200-60606600	Weak transcription	Lung	lung
11	chr5:60598600-60600600	Weak transcription	Brain Substantia Nigra	brain
12	chr5:60598600-60601400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr5:60598600-60601600	Enhancers	HepG2	liver
14	chr5:60598600-60602200	Weak transcription	Esophagus	oesophagus
15	chr5:60598800-60600600	Weak transcription	Brain Anterior Caudate	brain
16	chr5:60599000-60600600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr5:60599000-60600800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr5:60599200-60600600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:60599400-60600600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:60599400-60601000	Enhancers	Duodenum Mucosa	Duodenum
21	chr5:60599400-60603200	Enhancers	Fetal Intestine Large	intestine
22	chr5:60599400-60603400	Enhancers	Placenta	Placenta
23	chr5:60599600-60600600	Flanking Active TSS	NHEK	skin
24	chr5:60599600-60600800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:60599600-60600800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr5:60599600-60601200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:60599800-60600600	Weak transcription	Fetal Lung	lung
28	chr5:60599800-60600800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:60599800-60601000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:60599800-60601000	Active TSS	A549	lung
31	chr5:60599800-60601600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:60599800-60601600	Enhancers	Fetal Intestine Small	intestine
33	chr5:60599800-60601800	Weak transcription	GM12878-XiMat	blood
34	chr5:60599800-60602200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr5:60599800-60602400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:60600000-60603200	Enhancers	Stomach Mucosa	stomach
37	chr5:60600200-60600600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:60600200-60600600	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr5:60600200-60600800	Enhancers	Left Ventricle	heart
40	chr5:60600200-60600800	Enhancers	Right Atrium	heart
41	chr5:60600200-60601400	Flanking Active TSS	Hela-S3	cervix
42	chr5:60600400-60600600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr5:60600400-60600600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:60600400-60600600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:60600400-60600600	Enhancers	Colonic Mucosa	Colon
46	chr5:60600400-60600600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr5:60600400-60600600	Enhancers	Ovary	ovary
48	chr5:60600400-60600600	Enhancers	Pancreas	Pancrea
49	chr5:60600400-60600600	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr5:60600400-60600600	Enhancers	Small Intestine	intestine

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