Variant report

Variant	rs27552
Chromosome Location	chr5:16711451-16711452
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16710425..16712025-chr5:16715112..16717325,2	MCF-7	breast:
2	chr5:16710355..16712259-chr5:16729265..16730891,2	MCF-7	breast:
3	chr5:16710511..16712178-chr5:16712556..16714357,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs152726	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs153182	0.83[EUR][1000 genomes]
rs153184	0.84[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs153185	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17501392	0.81[CHB][hapmap];0.80[CHD][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap]
rs193924	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs250343	0.80[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs31290	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs31297	0.82[ASN][1000 genomes]
rs31299	0.88[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs31497	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39887	0.85[JPT][hapmap]
rs39889	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs40979	0.84[GIH][hapmap]
rs42564	0.87[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv880373	chr5:16710572-16785604	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16663000-16712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:16663800-16713400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:16673800-16713400	Weak transcription	Psoas Muscle	Psoas
4	chr5:16675800-16713600	Weak transcription	Left Ventricle	heart
5	chr5:16681600-16713200	Weak transcription	Small Intestine	intestine
6	chr5:16682400-16736000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:16688000-16711600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:16690200-16713200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:16697200-16711600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:16701800-16711600	Strong transcription	Fetal Intestine Large	intestine
11	chr5:16701800-16713400	Weak transcription	Right Ventricle	heart
12	chr5:16702600-16711600	Strong transcription	HSMM	muscle
13	chr5:16703800-16711600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:16704200-16711600	Strong transcription	NHLF	lung
15	chr5:16704400-16711600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:16704600-16711600	Strong transcription	NH-A	brain
17	chr5:16705000-16711800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr5:16705000-16712400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:16705200-16713400	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:16705400-16711600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:16705600-16711600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:16705600-16712200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr5:16705800-16711800	Strong transcription	Fetal Intestine Small	intestine
24	chr5:16706800-16711600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:16706800-16711600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:16706800-16711600	Strong transcription	HUVEC	blood vessel
27	chr5:16707000-16711600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr5:16707200-16711600	Strong transcription	A549	lung
29	chr5:16707400-16711600	Strong transcription	NHEK	skin
30	chr5:16707600-16711600	Strong transcription	Placenta	Placenta
31	chr5:16709200-16711800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:16709200-16712800	Weak transcription	Liver	Liver
33	chr5:16709800-16713600	Weak transcription	Colonic Mucosa	Colon
34	chr5:16710000-16711600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:16710000-16712800	Enhancers	Brain Cingulate Gyrus	brain
36	chr5:16710400-16723600	Weak transcription	Esophagus	oesophagus
37	chr5:16710600-16711600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:16710600-16711600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:16710800-16711800	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:16711000-16711600	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:16711000-16712400	Weak transcription	NHDF-Ad	bronchial
42	chr5:16711000-16712800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:16711000-16713200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:16711200-16711600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:16711200-16711800	Enhancers	Brain Substantia Nigra	brain
46	chr5:16711200-16712400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:16711200-16712400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:16711200-16712400	Weak transcription	Adipose Nuclei	Adipose
49	chr5:16711200-16712400	Enhancers	Brain Germinal Matrix	brain
50	chr5:16711200-16712400	Enhancers	Brain Hippocampus Middle	brain

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