Variant report

Variant	rs2562347
Chromosome Location	chr5:16893978-16893979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16892933..16897070-chr5:16897498..16901971,5	MCF-7	breast:
2	chr5:16893313..16896141-chr5:16935202..16937655,2	MCF-7	breast:
3	chr5:16893446..16895051-chr5:16936085..16937930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs253483	0.86[AMR][1000 genomes]
rs2560850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560851	0.86[CHB][hapmap]
rs2562339	0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562341	0.82[CHB][hapmap]
rs2562343	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562353	0.81[AMR][1000 genomes]
rs2625175	0.85[AMR][1000 genomes]
rs2914576	0.81[CHB][hapmap]

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	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	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
3	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
4	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
5	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
6	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
7	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:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16874000-16894600	Weak transcription	Esophagus	oesophagus
2	chr5:16880600-16894800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:16882000-16894200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:16882800-16895600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:16884400-16894800	Weak transcription	Psoas Muscle	Psoas
6	chr5:16885400-16894200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:16886200-16894400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:16887200-16894000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:16887400-16894200	Weak transcription	Placenta	Placenta
10	chr5:16887600-16894200	Weak transcription	Adipose Nuclei	Adipose
11	chr5:16888600-16894200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr5:16889800-16894000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:16890000-16894200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:16890200-16894200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:16890200-16894600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:16890400-16894600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:16890400-16894600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:16890400-16894800	Weak transcription	Fetal Stomach	stomach
19	chr5:16890600-16894000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:16890600-16894000	Weak transcription	NH-A	brain
21	chr5:16890600-16894000	Weak transcription	Osteobl	bone
22	chr5:16890600-16894400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr5:16890600-16894400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:16890600-16894600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:16890800-16894000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:16890800-16894200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:16890800-16894200	Weak transcription	HSMMtube	muscle
28	chr5:16891200-16894000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:16891200-16894200	Weak transcription	HSMM	muscle
30	chr5:16891200-16894200	Weak transcription	NHDF-Ad	bronchial
31	chr5:16891400-16894000	Weak transcription	NHEK	skin
32	chr5:16891400-16894200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:16891400-16894200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:16891400-16894800	Weak transcription	Ovary	ovary
35	chr5:16891600-16894400	Weak transcription	Spleen	Spleen
36	chr5:16891600-16894400	Weak transcription	NHLF	lung
37	chr5:16891600-16894800	Weak transcription	Lung	lung
38	chr5:16892000-16894200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:16892200-16894400	Weak transcription	Fetal Kidney	kidney
40	chr5:16892200-16894400	Weak transcription	Fetal Lung	lung
41	chr5:16892400-16894000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:16892400-16894000	Weak transcription	HUVEC	blood vessel
43	chr5:16892400-16894200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:16892400-16894200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:16892400-16894200	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:16892600-16894000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:16892600-16894000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:16892600-16894000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:16892600-16894200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:16892800-16894000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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