Variant report

Variant	rs7613144
Chromosome Location	chr3:81605179-81605180
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11917558	0.80[YRI][hapmap]
rs12631775	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12638726	0.94[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13059815	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13063700	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086984	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1381303	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1461606	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2307058	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]
rs2639611	0.94[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34567512	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6768895	0.94[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6769105	0.94[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6769140	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6769230	0.94[CEU][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6773695	0.94[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs6785586	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6798069	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6798900	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6800241	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6805105	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7610703	0.80[YRI][hapmap]
rs7616817	0.94[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7622741	0.94[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7631349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7637268	0.94[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7649028	0.94[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs820275	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9811029	0.94[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9811835	0.94[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9815059	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9820815	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9853643	0.94[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9862299	0.81[TSI][hapmap]

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
rs7613144	CACNA1F	trans	parietal	SCAN
rs7613144	MEST	trans	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81581600-81628200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:81582800-81613200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:81583400-81613200	Weak transcription	Lung	lung
4	chr3:81583600-81613200	Weak transcription	Primary T cells from cord blood	blood
5	chr3:81583600-81625600	Weak transcription	HUVEC	blood vessel
6	chr3:81583800-81608000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:81583800-81608000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:81584200-81636600	Weak transcription	Placenta	Placenta
9	chr3:81584600-81612200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:81584600-81613000	Weak transcription	Ovary	ovary
11	chr3:81584800-81610400	Weak transcription	HSMM	muscle
12	chr3:81586200-81610800	Weak transcription	Adipose Nuclei	Adipose
13	chr3:81588400-81612200	Weak transcription	Left Ventricle	heart
14	chr3:81597600-81613200	Weak transcription	Primary B cells from cord blood	blood
15	chr3:81598200-81625600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:81598800-81613200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:81599600-81607800	Strong transcription	Dnd41	blood
18	chr3:81600000-81612200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:81600000-81613400	Weak transcription	Right Ventricle	heart
20	chr3:81601000-81613200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:81601200-81611200	Weak transcription	Psoas Muscle	Psoas
22	chr3:81601200-81613200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:81601400-81610400	Weak transcription	NHDF-Ad	bronchial
24	chr3:81603200-81605200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:81603200-81605200	Enhancers	Liver	Liver
26	chr3:81603600-81726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:81603800-81606800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:81604000-81608000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:81604200-81606600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:81604200-81607000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:81604200-81610800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:81604200-81613200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:81604200-81613200	Weak transcription	Aorta	Aorta
34	chr3:81604200-81613800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:81604200-81641200	Weak transcription	HSMMtube	muscle
36	chr3:81604400-81606000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:81604400-81607800	Weak transcription	Spleen	Spleen
38	chr3:81604400-81608000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:81604400-81613200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:81604400-81613200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:81604400-81613800	Weak transcription	HepG2	liver
42	chr3:81604600-81611000	Weak transcription	Osteobl	bone
43	chr3:81604600-81613200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:81604600-81613200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:81604800-81610800	Weak transcription	NHLF	lung

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