Variant report

Variant	rs40979
Chromosome Location	chr5:16721306-16721307
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs152726	0.85[JPT][hapmap]
rs153184	0.92[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs153185	0.88[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs173738	0.89[LWK][hapmap]
rs17501392	0.92[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap]
rs250343	0.85[ASW][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs26740	0.84[LWK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs27552	0.84[GIH][hapmap]
rs31290	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs31293	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs31296	0.84[AFR][1000 genomes]
rs31297	0.84[AFR][1000 genomes]
rs31299	0.87[GIH][hapmap]
rs39887	0.94[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs42564	1.00[ASW][hapmap];0.94[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	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

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16682400-16736000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:16710400-16723600	Weak transcription	Esophagus	oesophagus
3	chr5:16711200-16723800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:16711200-16736400	Weak transcription	Hela-S3	cervix
5	chr5:16711400-16721600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:16711400-16724000	Weak transcription	Ovary	ovary
7	chr5:16711400-16727800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:16711400-16728200	Weak transcription	Spleen	Spleen
9	chr5:16711400-16730200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:16711400-16731800	Weak transcription	HMEC	breast
11	chr5:16711600-16721600	Weak transcription	NHEK	skin
12	chr5:16711600-16721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:16711600-16736000	Weak transcription	Placenta	Placenta
14	chr5:16713600-16721600	Weak transcription	Stomach Mucosa	stomach
15	chr5:16713800-16731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:16713800-16735600	Weak transcription	Colonic Mucosa	Colon
17	chr5:16714000-16721400	Weak transcription	HSMMtube	muscle
18	chr5:16714000-16721600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:16714000-16724000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:16714000-16726200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr5:16714000-16726200	Weak transcription	Left Ventricle	heart
22	chr5:16714000-16730200	Weak transcription	Osteobl	bone
23	chr5:16714200-16721400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:16714200-16721600	Weak transcription	Fetal Lung	lung
25	chr5:16714200-16721600	Weak transcription	A549	lung
26	chr5:16714200-16721600	Weak transcription	HSMM	muscle
27	chr5:16714200-16726200	Weak transcription	Fetal Kidney	kidney
28	chr5:16714200-16730400	Weak transcription	NHLF	lung
29	chr5:16714200-16736000	Weak transcription	NHDF-Ad	bronchial
30	chr5:16714400-16730000	Weak transcription	NH-A	brain
31	chr5:16714600-16721600	Weak transcription	Brain Angular Gyrus	brain
32	chr5:16714600-16722000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:16714600-16726400	Weak transcription	Brain Substantia Nigra	brain
34	chr5:16714600-16728200	Weak transcription	Psoas Muscle	Psoas
35	chr5:16714800-16721600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr5:16714800-16721600	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:16714800-16721800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:16715000-16725400	Weak transcription	HUVEC	blood vessel
39	chr5:16717600-16721800	Weak transcription	Brain Germinal Matrix	brain
40	chr5:16717800-16721600	Weak transcription	Fetal Brain Female	brain
41	chr5:16717800-16721800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr5:16718000-16722000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:16718400-16721600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:16718400-16721600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:16718800-16721400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr5:16719000-16722000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:16719400-16722400	Enhancers	Pancreas	Pancrea
48	chr5:16719400-16723000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr5:16719600-16721600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:16719600-16721600	Weak transcription	Lung	lung

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