Variant report

Variant	rs6493065
Chromosome Location	chr15:43064772-43064773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10467975	0.93[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs11070377	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070378	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11070380	0.81[YRI][hapmap]
rs11070382	0.93[ASW][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap]
rs11632809	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11853250	0.86[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];0.81[YRI][hapmap]
rs11854550	0.92[CEU][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12323990	0.94[LWK][hapmap];0.89[YRI][hapmap]
rs12591415	0.93[ASW][hapmap];0.81[LWK][hapmap];0.89[YRI][hapmap]
rs12592573	0.86[ASW][hapmap];0.86[LWK][hapmap];0.95[YRI][hapmap]
rs12594600	0.93[ASW][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12594696	0.93[ASW][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap]
rs12594699	0.89[AFR][1000 genomes]
rs12594724	0.83[AFR][1000 genomes]
rs12594765	0.86[ASW][hapmap];0.83[LWK][hapmap];0.95[YRI][hapmap]
rs16957031	0.89[YRI][hapmap]
rs16957037	0.94[LWK][hapmap];0.89[YRI][hapmap]
rs16957055	0.86[ASW][hapmap];0.94[LWK][hapmap];0.95[YRI][hapmap]
rs16957061	0.86[ASW][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap]
rs16957063	0.86[ASW][hapmap];0.97[LWK][hapmap];0.95[YRI][hapmap]
rs16957120	0.90[YRI][hapmap]
rs16957165	0.94[MKK][hapmap];0.85[YRI][hapmap]
rs16957244	0.92[ASW][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap]
rs16957250	0.86[GIH][hapmap]
rs16957264	0.88[CHB][hapmap];1.00[CHD][hapmap]
rs2139655	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2682073	0.86[ASW][hapmap];0.81[YRI][hapmap]
rs28437884	0.81[AFR][1000 genomes]
rs28542286	0.88[AFR][1000 genomes]
rs28722903	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34302400	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35554267	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3742992	0.95[YRI][hapmap]
rs3742995	0.86[ASW][hapmap];0.97[LWK][hapmap];0.95[YRI][hapmap]
rs4334272	0.93[ASW][hapmap];0.91[LWK][hapmap];0.94[YRI][hapmap]
rs4924696	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs58548142	0.81[AFR][1000 genomes]
rs7174028	0.93[ASW][hapmap];0.86[LWK][hapmap]
rs7178567	0.86[ASW][hapmap]
rs7181238	0.86[ASW][hapmap];1.00[CEU][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73410931	0.81[AFR][1000 genomes]
rs8024266	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8028167	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8028699	0.95[YRI][hapmap]
rs8030696	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8031767	0.93[ASW][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap]
rs8033336	0.86[ASW][hapmap];0.86[LWK][hapmap];0.95[YRI][hapmap]
rs8042738	0.84[EUR][1000 genomes]
rs8042980	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9920092	0.92[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9920562	0.93[ASW][hapmap];0.92[CEU][hapmap];0.84[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9920624	0.81[ASW][hapmap];0.92[CEU][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9920935	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6493065	CATSPER2P1	cis	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43029800-43071000	Weak transcription	Pancreas	Pancrea
2	chr15:43030000-43066200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr15:43030000-43067200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:43030000-43093600	Weak transcription	Colonic Mucosa	Colon
5	chr15:43038400-43067400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:43044800-43066400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:43045000-43065600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:43045400-43068000	Weak transcription	Fetal Heart	heart
9	chr15:43045600-43074400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:43045800-43064800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:43051800-43065200	Weak transcription	Placenta	Placenta
12	chr15:43051800-43066200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:43051800-43069400	Weak transcription	Gastric	stomach
14	chr15:43051800-43070600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:43051800-43074600	Weak transcription	Right Ventricle	heart
16	chr15:43051800-43075000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:43051800-43083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:43052000-43065800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:43052000-43065800	Weak transcription	Thymus	Thymus
20	chr15:43052000-43066000	Weak transcription	Spleen	Spleen
21	chr15:43052000-43066600	Weak transcription	Ovary	ovary
22	chr15:43052000-43074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:43053600-43112200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:43053800-43066400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:43054000-43066000	Weak transcription	Brain Angular Gyrus	brain
26	chr15:43054000-43066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:43054000-43066400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:43054000-43074600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:43054000-43080200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:43054600-43067200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:43054600-43068600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:43054800-43066400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:43054800-43067200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:43054800-43146000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:43055200-43066600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:43055400-43066000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr15:43055600-43066800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:43056200-43065800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr15:43056600-43065800	Weak transcription	Brain Germinal Matrix	brain
40	chr15:43056800-43066200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:43056800-43067200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:43056800-43068200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:43056800-43116800	Weak transcription	HepG2	liver
44	chr15:43057400-43066400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:43057600-43107000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:43060800-43122200	Weak transcription	GM12878-XiMat	blood
47	chr15:43061000-43067400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:43061200-43074600	Weak transcription	HSMMtube	muscle
49	chr15:43062200-43065800	Weak transcription	Brain Anterior Caudate	brain
50	chr15:43062200-43067200	Weak transcription	Osteobl	bone

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