Variant report

Variant	rs253475
Chromosome Location	chr5:16858860-16858861
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	chr5:16850266..16851821-chr5:16858055..16860279,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1483015	0.98[AFR][1000 genomes]
rs1564651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs253474	0.82[AFR][1000 genomes]
rs253477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59233189	1.00[AMR][1000 genomes]
rs7720898	1.00[AMR][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:53 , 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	chr5:16853000-16860600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:16854000-16859000	Weak transcription	Fetal Intestine Large	intestine
5	chr5:16854000-16862600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:16855000-16859000	Enhancers	Fetal Stomach	stomach
7	chr5:16855800-16863000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:16856000-16861800	Weak transcription	Pancreas	Pancrea
9	chr5:16856000-16862200	Weak transcription	Ovary	ovary
10	chr5:16856000-16863000	Weak transcription	Gastric	stomach
11	chr5:16856000-16867000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:16856200-16862800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:16856400-16860000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:16856400-16864600	Weak transcription	NH-A	brain
15	chr5:16856600-16862200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:16856800-16863000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:16857000-16860800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:16857000-16862200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:16857000-16863000	Weak transcription	Osteobl	bone
20	chr5:16857200-16859200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:16857400-16863000	Weak transcription	HSMM	muscle
22	chr5:16857400-16870200	Weak transcription	HMEC	breast
23	chr5:16857600-16859000	Enhancers	Fetal Muscle Trunk	muscle
24	chr5:16857600-16860200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:16857800-16859000	Strong transcription	Fetal Intestine Small	intestine
26	chr5:16858000-16859200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:16858000-16859200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:16858000-16859800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:16858000-16861800	Weak transcription	HSMMtube	muscle
30	chr5:16858000-16862800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr5:16858000-16863000	Weak transcription	NHDF-Ad	bronchial
32	chr5:16858200-16859000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:16858200-16859200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:16858200-16859200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:16858200-16859200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:16858200-16859200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr5:16858200-16859200	Weak transcription	NHEK	skin
38	chr5:16858200-16860200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:16858200-16860400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:16858200-16860600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:16858200-16863200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:16858200-16863200	Weak transcription	NHLF	lung
43	chr5:16858200-16864400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:16858200-16864400	Weak transcription	Fetal Brain Male	brain
45	chr5:16858200-16871400	Weak transcription	HUVEC	blood vessel
46	chr5:16858400-16859000	Weak transcription	Fetal Muscle Leg	muscle
47	chr5:16858600-16859200	Weak transcription	A549	lung
48	chr5:16858600-16859400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:16858600-16862200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:16858600-16862400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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