Variant report

Variant	rs7172489
Chromosome Location	chr15:59550008-59550009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs3794488	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57487429	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58579379	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59773793	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62002697	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494079	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6494080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6494084	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494086	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494087	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6494089	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172761	0.92[ASN][1000 genomes]
rs7174147	0.92[ASN][1000 genomes]
rs7175876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7179352	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181249	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027055	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8027766	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8038705	0.86[EUR][1000 genomes]
rs8040147	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv904273	chr15:59518488-59567137	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59515800-59566600	Weak transcription	Pancreas	Pancrea
2	chr15:59517800-59564200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr15:59521600-59566400	Weak transcription	Psoas Muscle	Psoas
4	chr15:59524600-59569200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:59524600-59574600	Weak transcription	Lung	lung
6	chr15:59525200-59554000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:59525200-59566600	Weak transcription	Small Intestine	intestine
8	chr15:59525200-59582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:59530600-59558200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:59530600-59568000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:59530800-59569000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:59533400-59559800	Weak transcription	NHLF	lung
13	chr15:59533400-59564000	Weak transcription	Ovary	ovary
14	chr15:59533400-59566800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:59536600-59559000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:59540000-59551200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:59540000-59560000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:59540000-59568800	Weak transcription	Fetal Kidney	kidney
19	chr15:59540400-59552600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:59540600-59561400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:59541000-59554000	Weak transcription	Right Ventricle	heart
22	chr15:59541000-59558000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:59541200-59566400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:59542200-59550600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:59542400-59551600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:59542400-59568200	Weak transcription	Gastric	stomach
27	chr15:59542600-59559800	Weak transcription	Spleen	Spleen
28	chr15:59542600-59563000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:59542800-59565400	Weak transcription	Left Ventricle	heart
30	chr15:59543200-59552400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:59543200-59553600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:59543200-59568200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:59543600-59551400	Weak transcription	NHDF-Ad	bronchial
34	chr15:59543800-59550600	Weak transcription	Brain Substantia Nigra	brain
35	chr15:59544000-59566200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr15:59544600-59582400	Weak transcription	Primary B cells from cord blood	blood
37	chr15:59544800-59552800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:59545000-59560000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:59545200-59557000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr15:59546400-59552800	Strong transcription	Osteobl	bone
41	chr15:59546600-59551000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:59546600-59551400	Enhancers	Liver	Liver
43	chr15:59546600-59551600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:59546800-59551600	Strong transcription	GM12878-XiMat	blood
45	chr15:59547400-59559600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:59547400-59564000	Weak transcription	Fetal Stomach	stomach
47	chr15:59547400-59587000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:59547800-59551400	Strong transcription	HSMMtube	muscle
49	chr15:59547800-59552600	Strong transcription	HMEC	breast
50	chr15:59548000-59552200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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