Variant report

Variant	rs10041973
Chromosome Location	chr5:60576278-60576279
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	chr5:60568345..60570305-chr5:60576207..60578303,2	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]
rs10044683	0.88[ASW][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs10056472	0.91[ASN][1000 genomes]
rs10070347	0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs10079115	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10471269	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs10471511	0.82[AFR][1000 genomes]
rs10939894	0.93[ASN][1000 genomes]
rs10939895	0.95[ASN][1000 genomes]
rs10939896	0.85[AFR][1000 genomes]
rs11747588	0.95[ASN][1000 genomes]
rs11949390	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs11960587	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12187377	0.84[LWK][hapmap]
rs12189420	0.86[EUR][1000 genomes]
rs12696981	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12696982	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13156118	0.83[ASN][1000 genomes]
rs13167234	0.89[ASN][1000 genomes]
rs13167244	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13167246	0.82[ASN][1000 genomes]
rs13179814	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13187871	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13355792	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4235485	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4315878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4379148	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4640746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700415	0.89[ASN][1000 genomes]
rs62366231	1.00[ASN][1000 genomes]
rs62366234	0.86[ASN][1000 genomes]
rs6449523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67749311	0.91[ASN][1000 genomes]
rs6869396	0.84[AFR][1000 genomes]
rs6892128	1.00[MEX][hapmap]
rs72759289	0.86[ASN][1000 genomes]
rs72759299	0.95[ASN][1000 genomes]
rs72761408	0.86[ASN][1000 genomes]
rs7721603	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][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	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	nsv823088	chr5:60572580-60577406	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv441955	chr5:60573147-60576860	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60567800-60577200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr5:60571200-60576600	Weak transcription	Pancreas	Pancrea
3	chr5:60571800-60583800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:60572000-60577000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:60572000-60582400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:60573400-60586600	Weak transcription	Esophagus	oesophagus
7	chr5:60573400-60594800	Weak transcription	Right Atrium	heart
8	chr5:60573800-60576600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:60574000-60576600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:60574000-60585400	Weak transcription	Spleen	Spleen
11	chr5:60574600-60576800	Enhancers	Small Intestine	intestine
12	chr5:60574600-60577600	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr5:60575200-60577400	Enhancers	Fetal Heart	heart
14	chr5:60575400-60576800	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr5:60575400-60577400	Enhancers	Fetal Intestine Small	intestine
16	chr5:60575400-60577400	Enhancers	HMEC	breast
17	chr5:60575400-60577800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:60575400-60577800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:60575400-60577800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:60575600-60576800	Enhancers	Stomach Smooth Muscle	stomach
21	chr5:60575600-60577000	Enhancers	NHLF	lung
22	chr5:60575600-60577200	Enhancers	Primary B cells from peripheral blood	blood
23	chr5:60575600-60577200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:60575600-60577200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr5:60575600-60577200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr5:60575600-60577200	Enhancers	HSMM	muscle
27	chr5:60575600-60577200	Enhancers	Osteobl	bone
28	chr5:60575600-60577400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr5:60575600-60577400	Enhancers	Brain Germinal Matrix	brain
30	chr5:60575600-60577400	Enhancers	Fetal Intestine Large	intestine
31	chr5:60575600-60577800	Enhancers	HUVEC	blood vessel
32	chr5:60575800-60576600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:60575800-60576800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr5:60575800-60576800	Enhancers	HSMMtube	muscle
35	chr5:60575800-60577000	Enhancers	Rectal Smooth Muscle	rectum
36	chr5:60575800-60577200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:60575800-60577200	Enhancers	Primary hematopoietic stem cells	blood
38	chr5:60575800-60577200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:60575800-60577400	Enhancers	Primary B cells from cord blood	blood
40	chr5:60575800-60577400	Enhancers	A549	lung
41	chr5:60575800-60577400	Enhancers	NHDF-Ad	bronchial
42	chr5:60575800-60577600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:60575800-60577800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:60576000-60576400	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr5:60576000-60576400	Flanking Active TSS	NH-A	brain
46	chr5:60576000-60576600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:60576000-60576600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:60576000-60576600	Enhancers	Placenta Amnion	Placenta Amnion
49	chr5:60576000-60576800	Enhancers	Fetal Lung	lung
50	chr5:60576000-60576800	Enhancers	Psoas Muscle	Psoas

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