Variant report

Variant	rs12916237
Chromosome Location	chr15:57249294-57249295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57208582..57210610-chr15:57249153..57251996,2	K562	blood:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10518894	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10518895	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11071305	0.83[EUR][1000 genomes]
rs11630195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631541	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11631732	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632592	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11852340	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11853331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs11855648	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11858471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898327	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12898844	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12899187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12899915	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12900589	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12900874	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12900986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901780	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12904070	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12904784	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12905900	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12906873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906936	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12908670	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909811	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12910094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes]
rs12914182	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12914410	0.82[AMR][1000 genomes]
rs12914625	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12916958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12917247	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13313455	0.82[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1430823	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1628067	0.84[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17239040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17819700	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1820995	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2053472	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2111891	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2116065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213149	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]
rs213164	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2165461	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2169466	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2414490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2414494	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2464429	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2464430	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2470079	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2470082	0.89[JPT][hapmap]
rs2583108	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2585082	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2585087	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2585088	0.90[JPT][hapmap]
rs2585102	0.81[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2585112	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2615231	0.81[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2703576	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2703580	0.89[JPT][hapmap]
rs2733170	0.89[JPT][hapmap]
rs2733171	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2733174	0.81[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733176	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733181	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2733188	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2733332	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs2920267	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs2951901	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs2951903	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2951904	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2962990	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs2962991	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2962992	0.82[JPT][hapmap]
rs2962993	0.81[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34262415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35646942	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3803455	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4399497	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4774898	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4774899	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774910	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs62022986	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62022988	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62025331	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493901	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs715338	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7170133	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7175436	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs7496293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8037901	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs967514	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]

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:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
2	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:57222600-57250200	Weak transcription	NH-A	brain
4	chr15:57222800-57255000	Weak transcription	HMEC	breast
5	chr15:57227000-57249800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:57227600-57260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:57228200-57260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:57229400-57255800	Weak transcription	Fetal Stomach	stomach
9	chr15:57232000-57256000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:57233000-57250200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:57236800-57249800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:57238400-57256200	Weak transcription	K562	blood
13	chr15:57239600-57250200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:57240200-57250200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:57240200-57250200	Weak transcription	Left Ventricle	heart
16	chr15:57241000-57255600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:57241200-57251600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:57241200-57254400	Weak transcription	NHLF	lung
19	chr15:57242200-57249800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:57242200-57251400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:57242200-57256000	Weak transcription	Ovary	ovary
22	chr15:57242400-57250000	Weak transcription	Thymus	Thymus
23	chr15:57242600-57252000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:57244000-57255800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:57244200-57257800	Weak transcription	Fetal Intestine Small	intestine
26	chr15:57246800-57256000	Weak transcription	Gastric	stomach
27	chr15:57247000-57249400	ZNF genes & repeats	Fetal Lung	lung
28	chr15:57248200-57249800	Enhancers	HepG2	liver
29	chr15:57248200-57250800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr15:57248600-57249400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr15:57248600-57251800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr15:57248800-57251800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr15:57249000-57249400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
34	chr15:57249000-57252000	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr15:57249200-57249400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:57249200-57249400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
37	chr15:57249200-57249400	ZNF genes & repeats	Primary B cells from cord blood	blood
38	chr15:57249200-57249400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:57249200-57249400	ZNF genes & repeats	Aorta	Aorta
40	chr15:57249200-57249400	Genic enhancers	Fetal Thymus	thymus
41	chr15:57249200-57249400	Enhancers	Psoas Muscle	Psoas
42	chr15:57249200-57249400	Enhancers	Right Ventricle	heart
43	chr15:57249200-57249400	ZNF genes & repeats	Osteobl	bone
44	chr15:57249200-57249600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr15:57249200-57249800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:57249200-57249800	Enhancers	A549	lung
47	chr15:57249200-57251600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:57249200-57252400	Enhancers	Dnd41	blood

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