Variant report

Variant	rs17460201
Chromosome Location	chr15:76673627-76673628
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	chr15:76668083..76670224-chr15:76672287..76674754,2	MCF-7	breast:
2	chr15:76630618..76633246-chr15:76671829..76673785,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs11072580	0.88[JPT][hapmap]
rs11072599	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1117367	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1125932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12148786	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs12148805	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12437627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs12438077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12439484	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs12440151	0.81[AFR][1000 genomes]
rs12440815	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441247	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12441433	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12441550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12442266	0.82[JPT][hapmap]
rs12443137	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12591100	0.81[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs12592171	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12592386	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592420	0.89[ASN][1000 genomes]
rs12592501	0.91[ASW][hapmap]
rs12593751	0.86[ASN][1000 genomes]
rs12594577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12595211	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs12595717	1.00[YRI][hapmap]
rs12595738	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs12898415	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs12899871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12902414	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12902506	1.00[ASW][hapmap]
rs12907668	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12907805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908334	0.88[JPT][hapmap]
rs12913096	1.00[ASW][hapmap];0.83[JPT][hapmap]
rs12914005	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915248	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12916573	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12917430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157783	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs1587381	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1588961	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1603856	1.00[YRI][hapmap]
rs16967958	1.00[YRI][hapmap]
rs17361504	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs17362383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363364	1.00[YRI][hapmap]
rs17363713	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17364076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17364330	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17364714	1.00[YRI][hapmap]
rs17458234	1.00[YRI][hapmap]
rs17461634	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1874944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1875884	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875885	0.92[CEU][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1946650	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1965492	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2117369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2120107	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs2120108	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2164101	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2176623	1.00[ASW][hapmap];0.83[JPT][hapmap]
rs2404740	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2469542	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs2469565	0.82[CEU][hapmap]
rs284895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3759853	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs3866543	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4079681	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4633676	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4886496	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886799	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4886801	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4886813	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs56089215	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56216512	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56351018	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs58511211	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs58684938	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59088060	0.81[AFR][1000 genomes]
rs66754747	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs66986092	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67232575	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67263359	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67418609	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67888330	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67920045	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7162455	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7163946	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7164060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7164813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7165025	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7174889	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7174953	0.81[AFR][1000 genomes]
rs7179142	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7403276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs744336	0.95[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes]
rs8025134	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8030411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8039545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8043057	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs959991	0.91[ASW][hapmap]
rs9646213	0.85[EUR][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	nsv510667	chr15:76653359-76708310	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17460201	SCAPER	cis	parietal	SCAN
rs17460201	ZNF291	cis	multi-tissue	Pritchard
rs17460201	NRG4	cis	parietal	SCAN
rs17460201	SCAPER	cis	lung	GTEx
rs17460201	SCAPER	cis	Nerve Tibial	GTEx
rs17460201	STOML1	cis	cerebellum	SCAN
rs17460201	SCAPER	cis	cerebellum	SCAN
rs17460201	SCAPER	cis	Artery Tibial	GTEx
rs17460201	SCAPER	cis	Thyroid	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76639800-76682600	Weak transcription	Pancreas	Pancrea
2	chr15:76639800-76695400	Weak transcription	Spleen	Spleen
3	chr15:76639800-76727400	Weak transcription	Right Ventricle	heart
4	chr15:76640800-76694600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:76641400-76694600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:76642800-76693800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:76643800-76695000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:76645800-76686200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:76646600-76695400	Weak transcription	Ovary	ovary
10	chr15:76648400-76674400	Weak transcription	Brain Substantia Nigra	brain
11	chr15:76650800-76674000	Weak transcription	Small Intestine	intestine
12	chr15:76652400-76675200	Weak transcription	Brain Germinal Matrix	brain
13	chr15:76657400-76674000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr15:76660200-76674400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:76660600-76674000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:76660800-76693600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:76661000-76674200	Weak transcription	Lung	lung
18	chr15:76661000-76675600	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:76661000-76676400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:76661000-76685800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:76661000-76695200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:76661000-76695400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:76661000-76695400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:76661000-76708600	Weak transcription	Brain Anterior Caudate	brain
25	chr15:76661200-76675400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:76661200-76698000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:76661200-76710800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:76661600-76698000	Weak transcription	Dnd41	blood
29	chr15:76662200-76674800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:76662400-76679000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr15:76662400-76695400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr15:76662800-76679200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr15:76664800-76698000	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:76665400-76674800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:76666200-76673800	Weak transcription	Aorta	Aorta
36	chr15:76666200-76674400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr15:76666200-76679400	Weak transcription	Placenta	Placenta
38	chr15:76666200-76694600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:76666200-76696200	Weak transcription	Brain Angular Gyrus	brain
40	chr15:76666200-76706800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:76666400-76694600	Weak transcription	Adipose Nuclei	Adipose
42	chr15:76666400-76695200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:76666400-76695400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:76666400-76698200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:76666600-76695200	Weak transcription	Fetal Muscle Leg	muscle
46	chr15:76667200-76681600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:76668800-76673800	Weak transcription	Left Ventricle	heart
48	chr15:76668800-76679600	Weak transcription	Thymus	Thymus
49	chr15:76668800-76695000	Weak transcription	Fetal Brain Female	brain
50	chr15:76668800-76695400	Weak transcription	Fetal Muscle Trunk	muscle

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