Variant report

Variant	rs12901780
Chromosome Location	chr15:57258531-57258532
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11071305	0.81[EUR][1000 genomes]
rs11630195	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11631228	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11631541	0.88[AMR][1000 genomes]
rs11631732	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11632592	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11853331	0.81[AMR][1000 genomes]
rs11858471	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12898327	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12898844	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12899187	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899915	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12900986	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12903578	0.82[AMR][1000 genomes]
rs12904070	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12904784	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12905900	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12906873	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12906936	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12908670	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909811	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12910094	0.84[AMR][1000 genomes]
rs12914182	0.81[AMR][1000 genomes]
rs12914410	0.82[AMR][1000 genomes]
rs12914625	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916237	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916958	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12917247	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1430823	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1628067	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17239040	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17819700	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2053472	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2111891	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2116065	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2116066	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213164	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2165461	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2414490	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2414494	0.83[AMR][1000 genomes]
rs2583108	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2585082	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2585087	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2585102	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2733171	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2733174	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2733176	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2733181	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2962993	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34262415	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35646942	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3803454	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803455	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4399497	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774898	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4774899	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4774902	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62022986	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62022988	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62025331	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs715338	0.88[ASN][1000 genomes]
rs7170133	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7496293	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57227600-57260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:57228200-57260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:57251000-57259200	Weak transcription	Right Atrium	heart
4	chr15:57251000-57260600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:57251000-57261000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:57251800-57260800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:57253800-57259000	Enhancers	A549	lung
8	chr15:57254400-57259000	Enhancers	Brain Substantia Nigra	brain
9	chr15:57254400-57259000	Enhancers	HepG2	liver
10	chr15:57254800-57259000	Enhancers	Brain Hippocampus Middle	brain
11	chr15:57255000-57259000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:57255000-57259800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:57256200-57260800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:57256200-57260800	Weak transcription	Stomach Mucosa	stomach
15	chr15:57256200-57263400	Weak transcription	Lung	lung
16	chr15:57256200-57264400	Weak transcription	NH-A	brain
17	chr15:57256200-57265200	Weak transcription	Fetal Brain Male	brain
18	chr15:57256200-57265800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:57256400-57260000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:57256400-57261400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:57256400-57263600	Weak transcription	Brain Germinal Matrix	brain
22	chr15:57256400-57264000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:57256400-57265200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr15:57256600-57259000	Enhancers	Primary T cells from cord blood	blood
25	chr15:57256600-57260800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:57256800-57258600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:57256800-57259000	Weak transcription	Left Ventricle	heart
28	chr15:57256800-57259600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:57256800-57259600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:57256800-57259600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:57256800-57259600	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:57256800-57259600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:57256800-57259600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:57256800-57259600	Weak transcription	Right Ventricle	heart
35	chr15:57256800-57259600	Weak transcription	Thymus	Thymus
36	chr15:57256800-57259600	Weak transcription	K562	blood
37	chr15:57256800-57259800	Weak transcription	Brain Angular Gyrus	brain
38	chr15:57256800-57259800	Weak transcription	Ovary	ovary
39	chr15:57256800-57260200	Weak transcription	Pancreas	Pancrea
40	chr15:57256800-57260200	Weak transcription	Psoas Muscle	Psoas
41	chr15:57256800-57260600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:57256800-57260600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:57256800-57260600	Weak transcription	Gastric	stomach
44	chr15:57256800-57260600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:57256800-57260600	Weak transcription	Dnd41	blood
46	chr15:57256800-57260600	Weak transcription	HMEC	breast
47	chr15:57256800-57260800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr15:57256800-57260800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:57256800-57260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:57256800-57261000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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