Variant report

Variant	rs253474
Chromosome Location	chr5:16860851-16860852
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	chr5:16860814..16863771-chr5:16866048..16868636,3	MCF-7	breast:
2	chr5:16855463..16857293-chr5:16859556..16861090,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1483015	0.83[YRI][hapmap]
rs1564651	0.82[AFR][1000 genomes]
rs253475	0.82[AFR][1000 genomes]
rs253477	0.82[AFR][1000 genomes]
rs2560857	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs2560859	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1026773	chr5:16846836-16877367	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1034844	chr5:16854341-16903100	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16839000-16864600	Weak transcription	Fetal Brain Female	brain
2	chr5:16842400-16862800	Weak transcription	Stomach Mucosa	stomach
3	chr5:16854000-16862600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:16855800-16863000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:16856000-16861800	Weak transcription	Pancreas	Pancrea
6	chr5:16856000-16862200	Weak transcription	Ovary	ovary
7	chr5:16856000-16863000	Weak transcription	Gastric	stomach
8	chr5:16856000-16867000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:16856200-16862800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:16856400-16864600	Weak transcription	NH-A	brain
11	chr5:16856600-16862200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:16856800-16863000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:16857000-16862200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:16857000-16863000	Weak transcription	Osteobl	bone
15	chr5:16857400-16863000	Weak transcription	HSMM	muscle
16	chr5:16857400-16870200	Weak transcription	HMEC	breast
17	chr5:16858000-16861800	Weak transcription	HSMMtube	muscle
18	chr5:16858000-16862800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:16858000-16863000	Weak transcription	NHDF-Ad	bronchial
20	chr5:16858200-16863200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:16858200-16863200	Weak transcription	NHLF	lung
22	chr5:16858200-16864400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:16858200-16864400	Weak transcription	Fetal Brain Male	brain
24	chr5:16858200-16871400	Weak transcription	HUVEC	blood vessel
25	chr5:16858600-16862200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:16858600-16862400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:16858800-16862000	Weak transcription	Fetal Lung	lung
28	chr5:16859000-16861000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:16859200-16865600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:16859400-16861000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:16859600-16862400	Weak transcription	Fetal Intestine Large	intestine
32	chr5:16859600-16864600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr5:16859800-16862400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:16859800-16862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:16859800-16863000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:16859800-16863200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr5:16859800-16864600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:16859800-16866400	Weak transcription	Fetal Intestine Small	intestine
39	chr5:16859800-16869600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:16860000-16861200	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr5:16860200-16861000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr5:16860200-16861200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr5:16860200-16861200	Enhancers	H9 Cell Line	embryonic stem cell
44	chr5:16860200-16861200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr5:16860400-16861200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr5:16860600-16861000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr5:16860600-16861000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr5:16860600-16861000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr5:16860600-16861000	Enhancers	Fetal Kidney	kidney
50	chr5:16860600-16861200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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