Variant report

Variant	rs12898415
Chromosome Location	chr15:76574232-76574233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76573019..76575613-chr15:76581006..76583116,2	K562	blood:
2	chr15:76573073..76575469-chr15:76605288..76607304,2	MCF-7	breast:
3	chr15:76572907..76574984-chr15:76602296..76604808,2	K562	blood:
4	chr15:76570469..76574475-chr15:76576214..76579233,4	K562	blood:
5	chr15:76571445..76574475-chr15:76576214..76578966,3	K562	blood:
6	chr15:76573739..76576523-chr15:76603684..76605605,3	K562	blood:
7	chr15:76572935..76575613-chr15:76581006..76583216,3	K562	blood:

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs11072576	0.89[CHB][hapmap]
rs11072579	0.87[CHB][hapmap]
rs11072580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072583	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs11072585	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs11072587	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs11634060	0.86[CHB][hapmap]
rs11636851	0.87[CHB][hapmap]
rs12050896	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs12438741	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12442266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592171	0.82[CEU][hapmap];0.87[JPT][hapmap]
rs12592501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12595211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12595717	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12595738	0.96[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12899871	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs12901160	0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12902506	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs12907668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12907805	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs12908334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12909718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12911035	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12913096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12915248	0.88[JPT][hapmap]
rs12916022	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1474117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1587381	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs16967958	1.00[YRI][hapmap]
rs16968083	0.87[CHB][hapmap]
rs17361504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17362383	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs17363364	1.00[YRI][hapmap]
rs17364076	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs17364330	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs17458234	1.00[YRI][hapmap]
rs17460201	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs1850722	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs1875885	1.00[YRI][hapmap]
rs1875888	0.85[CHB][hapmap]
rs2117369	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs2139190	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2176623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404974	0.80[ASN][1000 genomes]
rs2456045	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2456046	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2456050	0.86[CHB][hapmap]
rs2460154	0.92[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs2469541	1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs2469542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2469548	0.86[CHB][hapmap]
rs2469565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2469566	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs284895	0.88[JPT][hapmap]
rs2959850	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes]
rs2959853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34213321	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34893715	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35707798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784449	0.85[CHB][hapmap]
rs3866543	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3898352	0.87[CHB][hapmap]
rs4079681	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs4381566	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4633676	0.88[JPT][hapmap]
rs4886484	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4886485	0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4886488	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs4886777	0.86[CHB][hapmap]
rs4886779	0.81[CHB][hapmap]
rs4886783	0.86[CHB][hapmap]
rs4886787	0.86[CHB][hapmap]
rs4886788	0.86[CHB][hapmap]
rs4886789	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs4886791	0.86[CHB][hapmap]
rs4886799	0.88[JPT][hapmap]
rs4886801	0.88[JPT][hapmap]
rs55805818	0.82[ASN][1000 genomes]
rs67306087	0.91[AFR][1000 genomes]
rs7163946	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs7164060	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs7164813	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs7174889	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7177923	0.86[CHB][hapmap]
rs7179142	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs7180462	0.86[CHB][hapmap]
rs7403276	0.88[JPT][hapmap]
rs8028504	0.86[CHB][hapmap]
rs8029637	0.86[CHB][hapmap]
rs8030411	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs8030454	0.87[CHB][hapmap]
rs8033494	0.86[CHB][hapmap]
rs8039545	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs869452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs870295	0.86[CHB][hapmap]
rs879625	0.87[CHB][hapmap]
rs883993	0.86[CHB][hapmap]
rs937732	0.90[CHB][hapmap]
rs937733	0.87[CHB][hapmap]
rs959991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12898415	SCAPER	cis	lung	GTEx
rs12898415	SCAPER	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76550600-76578400	Strong transcription	Liver	Liver
2	chr15:76555800-76578800	Weak transcription	Psoas Muscle	Psoas
3	chr15:76555800-76579000	Weak transcription	NHLF	lung
4	chr15:76555800-76586000	Weak transcription	Stomach Mucosa	stomach
5	chr15:76556400-76581400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:76556800-76594600	Weak transcription	Esophagus	oesophagus
7	chr15:76557000-76582800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:76558000-76603000	Weak transcription	Aorta	Aorta
9	chr15:76560000-76582400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:76560200-76578600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:76561000-76574800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr15:76561000-76576200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:76561000-76580400	Strong transcription	Adipose Nuclei	Adipose
14	chr15:76561000-76587600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:76561200-76578400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:76561400-76578800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr15:76562000-76591600	Weak transcription	Small Intestine	intestine
18	chr15:76562600-76574600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:76562600-76586000	Weak transcription	Brain Angular Gyrus	brain
20	chr15:76562800-76574400	Weak transcription	Brain Substantia Nigra	brain
21	chr15:76562800-76580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:76563000-76574400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:76563000-76577000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:76563000-76578200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:76563000-76578400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr15:76563000-76579200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:76563000-76581800	Weak transcription	Fetal Brain Male	brain
28	chr15:76563000-76586400	Weak transcription	Fetal Heart	heart
29	chr15:76563200-76590800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:76564200-76574400	Weak transcription	NHEK	skin
31	chr15:76564200-76580600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:76565200-76581200	Strong transcription	HepG2	liver
33	chr15:76565200-76581400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:76566400-76579600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:76567600-76574600	Weak transcription	Gastric	stomach
36	chr15:76567600-76578200	Weak transcription	Brain Germinal Matrix	brain
37	chr15:76567600-76581800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:76568400-76578200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:76568600-76575000	Strong transcription	Primary T cells from cord blood	blood
40	chr15:76568800-76574400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:76568800-76575800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:76568800-76576400	Strong transcription	Fetal Thymus	thymus
43	chr15:76568800-76581600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:76569000-76580600	Strong transcription	Osteobl	bone
45	chr15:76569000-76585200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:76569000-76586400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr15:76569200-76576200	Strong transcription	HSMM	muscle
48	chr15:76569200-76576600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:76569200-76577200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:76569200-76580400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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