Variant report

Variant	rs2307058
Chromosome Location	chr3:81586439-81586440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1031265	0.85[JPT][hapmap]
rs11917558	0.83[CHB][hapmap]
rs12631775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637192	0.81[ASN][1000 genomes]
rs12638726	0.94[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13059815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13063700	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082939	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs13086984	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13087181	0.90[JPT][hapmap]
rs13088641	0.90[JPT][hapmap]
rs13092113	0.85[JPT][hapmap]
rs13097903	0.85[JPT][hapmap]
rs1381302	0.90[JPT][hapmap]
rs1381303	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1461606	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17019039	0.90[JPT][hapmap]
rs17019042	0.90[JPT][hapmap]
rs2639611	0.94[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34567512	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35058426	0.86[ASN][1000 genomes]
rs59299387	0.83[ASN][1000 genomes]
rs6764261	0.83[CHB][hapmap]
rs6768592	0.85[JPT][hapmap]
rs6768895	0.94[CEU][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6769105	0.94[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6769140	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6769230	0.94[CEU][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6773695	0.94[CEU][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs6785586	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6798069	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6798900	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6800241	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6805105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7610703	0.83[CHB][hapmap]
rs7613144	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7615728	0.85[ASN][1000 genomes]
rs7616817	0.94[CEU][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7618973	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs7622741	0.94[CEU][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631349	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7637268	0.94[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7649028	0.94[CEU][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820275	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9811029	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9811835	0.94[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9815059	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9818063	0.85[ASN][1000 genomes]
rs9820815	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9845467	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs9853643	0.94[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862299	0.81[TSI][hapmap]
rs9867226	0.86[ASN][1000 genomes]
rs9871529	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934018	chr3:81413060-81655338	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933756	chr3:81413060-81754738	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1003217	chr3:81435044-81752521	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv933259	chr3:81523854-81730617	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv999587	chr3:81534364-81707800	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv536603	chr3:81534364-81707800	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2307058	CACNA1F	trans	parietal	SCAN
rs2307058	MEST	trans	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81577400-81588400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:81577600-81586800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:81577600-81589800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:81580600-81589600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:81581000-81587600	Weak transcription	HepG2	liver
6	chr3:81581200-81588600	Strong transcription	Liver	Liver
7	chr3:81581400-81588000	Weak transcription	Esophagus	oesophagus
8	chr3:81581400-81593200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:81581600-81628200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:81582800-81591000	Strong transcription	Dnd41	blood
11	chr3:81582800-81592800	Weak transcription	Fetal Lung	lung
12	chr3:81582800-81597000	Weak transcription	Primary B cells from cord blood	blood
13	chr3:81582800-81613200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:81583000-81598200	Weak transcription	NH-A	brain
15	chr3:81583200-81596200	Weak transcription	Right Ventricle	heart
16	chr3:81583400-81591800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:81583400-81603800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:81583400-81613200	Weak transcription	Lung	lung
19	chr3:81583600-81586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:81583600-81596200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:81583600-81613200	Weak transcription	Primary T cells from cord blood	blood
22	chr3:81583600-81625600	Weak transcription	HUVEC	blood vessel
23	chr3:81583800-81587600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:81583800-81587800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:81583800-81599400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:81583800-81603400	Weak transcription	NHLF	lung
27	chr3:81583800-81608000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:81583800-81608000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:81584200-81587600	Weak transcription	Pancreas	Pancrea
30	chr3:81584200-81598600	Weak transcription	Osteobl	bone
31	chr3:81584200-81604000	Weak transcription	Aorta	Aorta
32	chr3:81584200-81636600	Weak transcription	Placenta	Placenta
33	chr3:81584400-81596400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:81584400-81603400	Weak transcription	HSMMtube	muscle
35	chr3:81584600-81587000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:81584600-81596400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:81584600-81598000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:81584600-81612200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:81584600-81613000	Weak transcription	Ovary	ovary
40	chr3:81584800-81596200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:81584800-81610400	Weak transcription	HSMM	muscle
42	chr3:81585200-81586600	Weak transcription	NHDF-Ad	bronchial
43	chr3:81585200-81588000	Weak transcription	Left Ventricle	heart
44	chr3:81585400-81596800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:81585400-81597200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:81585400-81599800	Weak transcription	Psoas Muscle	Psoas
47	chr3:81586200-81588400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:81586200-81595000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:81586200-81599400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:81586200-81610800	Weak transcription	Adipose Nuclei	Adipose

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