Variant report

Variant	rs7631349
Chromosome Location	chr3:81623527-81623528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031265	0.85[JPT][hapmap]
rs12631775	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12638726	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13059815	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13063700	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13082939	0.85[JPT][hapmap]
rs13086984	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1461606	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17019039	0.90[JPT][hapmap]
rs17019042	0.90[JPT][hapmap]
rs2307058	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]
rs2639611	0.94[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34567512	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35058426	0.82[ASN][1000 genomes]
rs6768592	0.85[JPT][hapmap]
rs6768895	0.94[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6769105	0.94[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6769140	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6769230	0.94[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6773695	0.94[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs6785586	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6798069	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6798900	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6800241	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6805105	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7613144	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]
rs7615728	0.82[ASN][1000 genomes]
rs7616817	0.94[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7618973	0.85[CHD][hapmap]
rs7622741	0.94[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637268	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7649028	0.94[CEU][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs820275	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9811029	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9811835	0.94[CEU][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9815059	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9818063	0.82[ASN][1000 genomes]
rs9820815	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9845467	0.85[CHD][hapmap]
rs9853643	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9862299	0.81[TSI][hapmap]
rs9867226	0.82[ASN][1000 genomes]
rs9871529	0.82[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
rs7631349	CACNA1F	trans	parietal	SCAN
rs7631349	MEST	trans	lymphoblastoid	seeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81581600-81628200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:81583600-81625600	Weak transcription	HUVEC	blood vessel
3	chr3:81584200-81636600	Weak transcription	Placenta	Placenta
4	chr3:81598200-81625600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:81603600-81726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:81604200-81641200	Weak transcription	HSMMtube	muscle
7	chr3:81608600-81644000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:81609200-81636600	Weak transcription	Pancreas	Pancrea
9	chr3:81609400-81635200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:81610800-81624000	Strong transcription	Dnd41	blood
11	chr3:81611600-81628600	Weak transcription	Spleen	Spleen
12	chr3:81611600-81629000	Weak transcription	NHLF	lung
13	chr3:81612000-81630400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:81612800-81626800	Weak transcription	Osteobl	bone
15	chr3:81612800-81631000	Weak transcription	Fetal Kidney	kidney
16	chr3:81613600-81625800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:81613600-81699200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:81614000-81625600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:81614000-81629600	Weak transcription	Psoas Muscle	Psoas
20	chr3:81614000-81638200	Weak transcription	Lung	lung
21	chr3:81614000-81693600	Weak transcription	Aorta	Aorta
22	chr3:81614200-81625800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:81614200-81627000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:81614200-81628800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:81614200-81640400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:81614400-81625600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:81614400-81625800	Weak transcription	Ovary	ovary
28	chr3:81614400-81627000	Weak transcription	HepG2	liver
29	chr3:81614400-81629600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:81614400-81643600	Weak transcription	Primary T cells from cord blood	blood
31	chr3:81614400-81688800	Weak transcription	Right Ventricle	heart
32	chr3:81614600-81625600	Weak transcription	Primary B cells from cord blood	blood
33	chr3:81614600-81633400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:81614600-81634200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:81614800-81625600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:81616000-81623600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:81617000-81623600	Weak transcription	GM12878-XiMat	blood
38	chr3:81617600-81623600	Weak transcription	Left Ventricle	heart
39	chr3:81617600-81631200	Weak transcription	Gastric	stomach
40	chr3:81618800-81629600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:81619000-81627000	Weak transcription	NHDF-Ad	bronchial
42	chr3:81621800-81629000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:81622000-81633000	Weak transcription	Hela-S3	cervix
44	chr3:81622200-81632600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:81622400-81641600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:81622600-81624000	Strong transcription	Liver	Liver
47	chr3:81622600-81629600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:81622600-81644600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:81622800-81625600	Weak transcription	HSMM	muscle
50	chr3:81622800-81643000	Weak transcription	Small Intestine	intestine

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