Variant report

Variant	rs6742445
Chromosome Location	chr2:58445873-58445874
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58444634..58446465-chr2:58458026..58460794,3	MCF-7	breast:
2	chr2:58444316..58447844-chr2:58463533..58467170,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10165760	0.89[AMR][1000 genomes]
rs10182762	0.89[AMR][1000 genomes]
rs1025755	0.89[AMR][1000 genomes]
rs11883874	0.89[AMR][1000 genomes]
rs11891477	0.89[AMR][1000 genomes]
rs11892302	0.89[AMR][1000 genomes]
rs11900900	1.00[AMR][1000 genomes]
rs11903212	0.96[AFR][1000 genomes]
rs13397947	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13405281	0.89[AMR][1000 genomes]
rs13410500	0.89[AMR][1000 genomes]
rs13422760	0.93[AFR][1000 genomes]
rs1371213	0.89[AMR][1000 genomes]
rs1404459	0.96[AFR][1000 genomes]
rs1404460	0.96[AFR][1000 genomes]
rs2165103	0.89[AMR][1000 genomes]
rs2312486	0.89[AMR][1000 genomes]
rs34335951	0.92[AFR][1000 genomes]
rs57112138	0.89[AMR][1000 genomes]
rs58470176	0.89[AMR][1000 genomes]
rs60364084	0.89[AMR][1000 genomes]
rs6709533	0.93[AFR][1000 genomes]
rs6740373	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6740836	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs716758	0.89[AMR][1000 genomes]
rs72948876	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951042	0.89[AMR][1000 genomes]
rs72951048	0.89[AMR][1000 genomes]
rs72951056	0.89[AMR][1000 genomes]
rs7340170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7590976	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7597069	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9309303	1.00[AMR][1000 genomes]
rs9973345	0.89[AMR][1000 genomes]
rs9973928	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:58391000-58467000	Weak transcription	HMEC	breast
3	chr2:58414000-58461400	Weak transcription	NHEK	skin
4	chr2:58416200-58454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:58421600-58452400	Weak transcription	NH-A	brain
7	chr2:58422000-58454200	Weak transcription	Left Ventricle	heart
8	chr2:58425600-58446600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:58425800-58446600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:58432000-58466400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:58433600-58454200	Weak transcription	Gastric	stomach
12	chr2:58437000-58460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:58437200-58459000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:58437800-58456800	Weak transcription	Fetal Kidney	kidney
15	chr2:58438600-58454200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:58438600-58454200	Weak transcription	Aorta	Aorta
17	chr2:58438600-58454200	Weak transcription	Esophagus	oesophagus
18	chr2:58438600-58454200	Weak transcription	Fetal Brain Female	brain
19	chr2:58438600-58454200	Weak transcription	Fetal Stomach	stomach
20	chr2:58438600-58454200	Weak transcription	Lung	lung
21	chr2:58438600-58454200	Weak transcription	Pancreas	Pancrea
22	chr2:58438600-58454200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:58438600-58454200	Weak transcription	Thymus	Thymus
24	chr2:58438600-58466400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:58438800-58454200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:58438800-58454200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:58439000-58446600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:58439000-58467400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:58439200-58454200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:58439200-58454400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:58439200-58457000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:58439200-58457600	Weak transcription	Placenta	Placenta
33	chr2:58439600-58454200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:58439800-58449200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:58440000-58454200	Weak transcription	Primary B cells from cord blood	blood
36	chr2:58440000-58465000	Weak transcription	Fetal Brain Male	brain
37	chr2:58440000-58467400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr2:58440600-58446600	Weak transcription	Fetal Thymus	thymus
39	chr2:58440600-58454200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:58440600-58454400	Weak transcription	HSMM	muscle
41	chr2:58440600-58462000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr2:58440600-58467400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:58440800-58449200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:58440800-58449400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:58440800-58450000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:58440800-58450400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:58440800-58453400	Weak transcription	NHDF-Ad	bronchial
48	chr2:58440800-58453600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:58440800-58454200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:58440800-58454400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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