Variant report

Variant	rs31299
Chromosome Location	chr5:16713465-16713466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs152726	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs153182	0.83[EUR][1000 genomes]
rs153184	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs153185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17501392	0.92[JPT][hapmap]
rs193924	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs250343	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs27552	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]
rs31290	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs31296	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs31297	0.86[ASN][1000 genomes]
rs31497	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39887	0.85[JPT][hapmap]
rs39888	0.83[EUR][1000 genomes]
rs39889	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40979	0.87[GIH][hapmap]
rs42564	0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.80[TSI][hapmap];0.87[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:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16675800-16713600	Weak transcription	Left Ventricle	heart
2	chr5:16682400-16736000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:16709800-16713600	Weak transcription	Colonic Mucosa	Colon
4	chr5:16710400-16723600	Weak transcription	Esophagus	oesophagus
5	chr5:16711200-16713600	Weak transcription	Aorta	Aorta
6	chr5:16711200-16713600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:16711200-16713600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:16711200-16719000	Weak transcription	Lung	lung
9	chr5:16711200-16719400	Weak transcription	Pancreas	Pancrea
10	chr5:16711200-16723800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:16711200-16736400	Weak transcription	Hela-S3	cervix
12	chr5:16711400-16713600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:16711400-16713600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:16711400-16717600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:16711400-16719400	Weak transcription	Gastric	stomach
16	chr5:16711400-16721000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:16711400-16721200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:16711400-16721600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:16711400-16724000	Weak transcription	Ovary	ovary
20	chr5:16711400-16727800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:16711400-16728200	Weak transcription	Spleen	Spleen
22	chr5:16711400-16730200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:16711400-16731800	Weak transcription	HMEC	breast
24	chr5:16711600-16713600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:16711600-16714200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:16711600-16721600	Weak transcription	NHEK	skin
27	chr5:16711600-16721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:16711600-16736000	Weak transcription	Placenta	Placenta
29	chr5:16711800-16713600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:16712200-16713600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr5:16712200-16714200	Enhancers	Fetal Lung	lung
32	chr5:16712400-16713600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr5:16712400-16713600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr5:16712400-16713600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:16712400-16713600	Enhancers	Fetal Intestine Small	intestine
36	chr5:16712400-16713600	Enhancers	Fetal Muscle Leg	muscle
37	chr5:16712400-16713800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:16712400-16714000	Enhancers	HSMMtube	muscle
39	chr5:16712400-16714200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:16712400-16714200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:16712400-16714200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:16712400-16714200	Enhancers	HSMM	muscle
43	chr5:16712400-16714400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr5:16712400-16715000	Enhancers	HUVEC	blood vessel
45	chr5:16712400-16715200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:16712600-16713600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr5:16712600-16713800	Active TSS	Brain Anterior Caudate	brain
48	chr5:16712600-16714200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:16712600-16714200	Strong transcription	A549	lung
50	chr5:16712600-16714400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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