Variant report

Variant	rs2562339
Chromosome Location	chr5:16885857-16885858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16883385..16886348-chr5:16888269..16889832,2	MCF-7	breast:
2	chr5:16882313..16886357-chr5:16933451..16937299,4	MCF-7	breast:
3	chr5:16877490..16879580-chr5:16883776..16886386,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2560850	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2560851	0.91[CHB][hapmap]
rs2562341	0.86[CHB][hapmap]
rs2562343	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562347	0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2914576	0.86[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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16867600-16889000	Weak transcription	Spleen	Spleen
2	chr5:16871200-16886000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:16873600-16886000	Weak transcription	Left Ventricle	heart
4	chr5:16874000-16894600	Weak transcription	Esophagus	oesophagus
5	chr5:16875600-16889000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:16877400-16888200	Weak transcription	HUVEC	blood vessel
7	chr5:16877400-16889000	Weak transcription	Fetal Stomach	stomach
8	chr5:16877800-16889000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:16878200-16893800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:16879200-16886800	Enhancers	Stomach Mucosa	stomach
11	chr5:16879600-16887600	Enhancers	HSMM	muscle
12	chr5:16880600-16894800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:16880800-16886400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:16881000-16889800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:16881400-16886000	Enhancers	HSMMtube	muscle
16	chr5:16881600-16886400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr5:16881800-16886000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:16881800-16888800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:16881800-16889000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:16881800-16889000	Weak transcription	Fetal Kidney	kidney
21	chr5:16881800-16889400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:16881800-16889800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:16882000-16894200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:16882200-16886000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:16882400-16889000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:16882600-16888800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:16882600-16889800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:16882800-16887000	Enhancers	NHDF-Ad	bronchial
29	chr5:16882800-16895600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:16883400-16886000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:16883400-16886000	Enhancers	Osteobl	bone
32	chr5:16883400-16887200	Enhancers	Ovary	ovary
33	chr5:16883400-16887600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:16883400-16889400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr5:16884000-16887400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:16884000-16887600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:16884000-16887600	Enhancers	Fetal Muscle Leg	muscle
38	chr5:16884000-16888200	Enhancers	Fetal Lung	lung
39	chr5:16884400-16886000	Weak transcription	Aorta	Aorta
40	chr5:16884400-16894800	Weak transcription	Psoas Muscle	Psoas
41	chr5:16884600-16886600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:16884600-16887400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:16884800-16886200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:16884800-16886400	Enhancers	Small Intestine	intestine
45	chr5:16884800-16886600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:16884800-16886800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr5:16884800-16887400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:16884800-16887400	Enhancers	NHLF	lung
49	chr5:16885000-16886000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr5:16885000-16887400	Enhancers	Placenta	Placenta

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