Variant report

Variant	rs1875888
Chromosome Location	chr15:76495005-76495006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76486525..76491130-chr15:76491292..76495169,6	MCF-7	breast:
2	chr15:76493051..76495991-chr15:76813493..76815400,2	MCF-7	breast:
3	chr15:76490388..76492553-chr15:76494551..76496076,2	MCF-7	breast:
4	chr15:76487373..76491413-chr15:76492592..76495149,4	K562	blood:
5	chr15:76493299..76496201-chr15:76496917..76499323,4	K562	blood:

Extended variants
information (count: 118 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs11072576	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072577	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072578	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072579	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072580	0.85[CHB][hapmap]
rs11072583	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072585	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072587	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11629459	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11631690	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631764	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11631874	0.84[EUR][1000 genomes]
rs11633405	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11634060	0.90[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11634472	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636278	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11636851	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637473	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11637855	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12050813	0.83[ASN][1000 genomes]
rs12050896	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12439484	0.84[CHB][hapmap]
rs12442266	0.85[CHB][hapmap]
rs12443449	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12592501	0.83[CHB][hapmap]
rs12595211	0.84[CHB][hapmap]
rs12595717	0.85[CHB][hapmap]
rs12898415	0.85[CHB][hapmap]
rs12902506	0.84[CHB][hapmap]
rs12907668	0.84[CHB][hapmap]
rs12908334	0.85[CHB][hapmap]
rs12909718	0.85[CHB][hapmap]
rs12913096	0.84[CHB][hapmap]
rs1474117	0.85[CHB][hapmap]
rs16968083	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17361504	0.84[CHB][hapmap]
rs1850722	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1875887	0.87[ASN][1000 genomes]
rs2007928	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2016734	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2139190	0.83[CHB][hapmap]
rs2176623	0.84[CHB][hapmap]
rs2404974	0.91[CEU][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2456046	0.84[CHB][hapmap]
rs2456049	0.89[ASN][1000 genomes]
rs2456050	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2456057	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2456071	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2469541	0.84[CHB][hapmap]
rs2469542	0.84[CHB][hapmap]
rs2469548	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2469565	0.81[CHB][hapmap]
rs2938697	0.86[ASN][1000 genomes]
rs2959850	0.89[CHB][hapmap]
rs2959853	0.84[CHB][hapmap]
rs35831705	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3759853	0.84[CHB][hapmap]
rs3784449	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3898352	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3915459	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3915460	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3927264	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3958426	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3991792	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3991793	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3991794	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4592616	0.88[EUR][1000 genomes]
rs4886484	0.85[CHB][hapmap]
rs4886486	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4886487	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4886488	0.84[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs4886777	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886779	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886781	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886783	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886784	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886787	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886788	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs4886789	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886791	0.90[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5012144	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55794488	0.80[AMR][1000 genomes]
rs55805818	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56737606	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57182285	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60017340	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60290059	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60371615	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60561507	0.89[AFR][1000 genomes]
rs61018254	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61275737	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61300240	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62027018	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62027047	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62027048	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62030232	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62030245	0.81[ASN][1000 genomes]
rs6495197	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7174889	0.84[CHB][hapmap]
rs7177923	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7179750	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7180462	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8028504	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8029637	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8030454	0.86[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8033494	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039063	0.90[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs869452	0.84[CHB][hapmap]
rs870295	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs879625	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs883993	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs937732	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs937733	0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959991	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1048760	chr15:76334544-76496977	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	nsv1054713	chr15:76460462-76505906	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1875888	ZNF291	cis	normal skin	skin_eQTL
rs1875888	ZNF291	cis	uninvolved skin	skin_eQTL
rs1875888	SCAPER	cis	Artery Tibial	GTEx
rs1875888	SCAPER	cis	lung	GTEx
rs1875888	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs1875888	ISL2	cis	Whole Blood	GTEx
rs1875888	SCAPER	cis	Whole Blood	GTEx
rs1875888	SCAPER	cis	Thyroid	GTEx
rs1875888	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1875888	SCAPER	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76484000-76498600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr15:76484000-76500800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:76484200-76498200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:76485400-76498400	Weak transcription	Fetal Brain Female	brain
5	chr15:76486800-76503000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:76486800-76516600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:76487000-76498200	Weak transcription	Primary T cells from cord blood	blood
8	chr15:76488800-76496200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:76489000-76498200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:76489400-76498000	Weak transcription	Brain Germinal Matrix	brain
11	chr15:76489400-76498800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:76489400-76502800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:76489400-76519800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:76489600-76496800	Weak transcription	Ovary	ovary
15	chr15:76489600-76498200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr15:76489600-76498400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr15:76489600-76498600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:76489600-76499800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:76489600-76500000	Weak transcription	Fetal Lung	lung
20	chr15:76489600-76501800	Weak transcription	GM12878-XiMat	blood
21	chr15:76489600-76503000	Weak transcription	Small Intestine	intestine
22	chr15:76489800-76496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:76489800-76498800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:76490000-76503600	Weak transcription	HUVEC	blood vessel
25	chr15:76490200-76496000	Weak transcription	Pancreas	Pancrea
26	chr15:76490200-76498000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:76490200-76498200	Weak transcription	Lung	lung
28	chr15:76490400-76497000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:76490400-76498200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:76490400-76501600	Weak transcription	Primary B cells from cord blood	blood
31	chr15:76490600-76498600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:76491200-76497400	Weak transcription	Gastric	stomach
33	chr15:76491200-76500600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:76491400-76495600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:76491400-76502800	Weak transcription	HMEC	breast
36	chr15:76491600-76498200	Weak transcription	Hela-S3	cervix
37	chr15:76491800-76495800	Weak transcription	A549	lung
38	chr15:76491800-76497200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:76491800-76498000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:76491800-76498000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:76491800-76498000	Weak transcription	NHEK	skin
42	chr15:76491800-76498600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:76491800-76500400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr15:76492000-76495400	Weak transcription	Adipose Nuclei	Adipose
45	chr15:76492000-76495600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:76492000-76495800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:76492000-76496000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:76492000-76497400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:76492000-76498000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:76492000-76498400	Weak transcription	Brain Substantia Nigra	brain

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