Variant report

Variant	rs41408650
Chromosome Location	chr15:52733250-52733251
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	chr15:52732225..52734502-chr15:52735586..52737887,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10518684	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs10518689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[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]
rs10518691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs10518692	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1058219	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap]
rs11853078	1.00[JPT][hapmap];0.85[YRI][hapmap]
rs11853114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs11853179	0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs11853337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11853586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11853954	0.84[TSI][hapmap]
rs11854130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11854247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11854673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11854780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11855082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11855257	0.80[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs11855453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11855584	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11855820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs11855884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11856588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11856662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11856752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11856810	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs11856896	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11857993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11858031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11858927	1.00[YRI][hapmap]
rs1464965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1464966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1474437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1474438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1693492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1693494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1693497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1693501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs1693502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs1693506	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[TSI][hapmap]
rs1693507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs1693508	0.86[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap]
rs1693524	0.80[CEU][hapmap]
rs1724595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs1724601	0.87[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs1724603	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1724608	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1724638	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs17613951	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17651326	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17651611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17651631	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs17707996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs17708103	0.93[CHB][hapmap]
rs1869126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1869127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1869128	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2140962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2177876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2257152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2272283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2290334	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs2414148	0.91[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2414152	0.84[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2693462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2899488	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3751619	0.83[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs3751620	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs3816449	0.91[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap]
rs4341694	0.91[ASW][hapmap];0.93[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs4774624	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4774625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4774627	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4776045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4776051	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4776053	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs940966	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs940971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs940972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs940973	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9788691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs41408650	ARPP19	cis	Nerve Tibial	GTEx
rs41408650	ARPP19	cis	lymphoblastoid	seeQTL
rs41408650	SMPD2	trans	parietal	SCAN
rs41408650	GNB5	cis	lymphoblastoid	seeQTL
rs41408650	MYO5A	cis	lymphoblastoid	seeQTL
rs41408650	ARPP19	cis	Artery Tibial	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
2	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
3	chr15:52697200-52738600	Weak transcription	Fetal Brain Female	brain
4	chr15:52702400-52737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:52721400-52737800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr15:52721400-52739000	Weak transcription	Primary B cells from cord blood	blood
7	chr15:52724600-52733600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:52728600-52737400	Weak transcription	Psoas Muscle	Psoas
9	chr15:52729000-52739400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr15:52729200-52734800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:52729800-52734800	Enhancers	Adipose Nuclei	Adipose
12	chr15:52730000-52734200	Enhancers	Brain Cingulate Gyrus	brain
13	chr15:52730000-52735600	Enhancers	Brain Anterior Caudate	brain
14	chr15:52730200-52734800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:52730400-52744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:52730600-52734200	Weak transcription	GM12878-XiMat	blood
17	chr15:52730600-52734400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:52730600-52736200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:52730600-52737200	Weak transcription	Right Ventricle	heart
20	chr15:52730600-52739400	Weak transcription	Esophagus	oesophagus
21	chr15:52730600-52741600	Weak transcription	Ovary	ovary
22	chr15:52730600-52741600	Weak transcription	HUVEC	blood vessel
23	chr15:52730600-52741800	Weak transcription	Gastric	stomach
24	chr15:52730800-52734200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:52730800-52735400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:52730800-52738000	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:52730800-52741800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr15:52731200-52733800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:52731200-52734400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr15:52731200-52734400	Weak transcription	Right Atrium	heart
31	chr15:52731600-52734400	Enhancers	Brain Angular Gyrus	brain
32	chr15:52731600-52734400	Enhancers	Brain Hippocampus Middle	brain
33	chr15:52731800-52734600	Enhancers	HMEC	breast
34	chr15:52731800-52734800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr15:52732200-52734600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr15:52732200-52734600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:52732200-52734600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:52732200-52734800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:52732200-52734800	Enhancers	A549	lung
40	chr15:52732200-52734800	Enhancers	HSMM	muscle
41	chr15:52732200-52734800	Enhancers	HSMMtube	muscle
42	chr15:52732200-52734800	Enhancers	NHEK	skin
43	chr15:52732400-52733800	Enhancers	NHDF-Ad	bronchial
44	chr15:52732400-52734200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:52732400-52734600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:52732400-52737200	Weak transcription	Left Ventricle	heart
47	chr15:52732600-52734000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:52732600-52734400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:52732600-52737200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:52732600-52750600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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