Variant report

Variant	rs7246657
Chromosome Location	chr19:37747108-37747109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1015849	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs10404920	0.86[CEU][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs10405064	0.86[CEU][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs10405407	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs10406177	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap]
rs10407084	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs10409204	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs10413389	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10414904	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs10415024	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs10415937	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs10417503	0.86[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs10417844	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs10418461	0.81[EUR][1000 genomes]
rs10418729	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10424574	0.86[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs12986220	0.87[EUR][1000 genomes]
rs13343471	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs13345116	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs1373991	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs1529957	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1559229	0.86[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap]
rs1823061	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2112923	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.96[YRI][hapmap]
rs2303131	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs2891699	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.96[YRI][hapmap]
rs35398388	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3745765	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs3760825	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.96[YRI][hapmap]
rs4417644	0.86[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs4452075	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs4803229	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs6508710	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508719	0.93[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap]
rs713256	0.86[CEU][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs7247259	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7247672	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7252346	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.96[YRI][hapmap]
rs7255972	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs7257672	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7258692	0.86[CEU][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs7259618	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7408563	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs8110011	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8111782	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs9304566	0.86[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs9917081	0.86[CEU][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
5	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
7	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
8	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv9717	chr19:37721760-37796698	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv960834	chr19:37742831-37749967	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	esv3520361	chr19:37745067-37811325	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv3520362	chr19:37745067-37811325	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	esv1832219	chr19:37747108-37793960	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coronary artery calcification	23870195	GWAS catalog

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7246657	BLVRB	cis	cerebellum	SCAN
rs7246657	LTBP4	cis	cerebellum	SCAN
rs7246657	EXOSC5	cis	cerebellum	SCAN
rs7246657	MEGF8	cis	cerebellum	SCAN
rs7246657	CBLC	cis	parietal	SCAN
rs7246657	VASP	cis	parietal	SCAN
rs7246657	PLEKHG2	cis	cerebellum	SCAN
rs7246657	DMPK	cis	parietal	SCAN
rs7246657	LIPE	cis	cerebellum	SCAN
rs7246657	PAFAH1B3	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37741600-37749200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr19:37743600-37747200	Weak transcription	Fetal Stomach	stomach
3	chr19:37743600-37749600	Weak transcription	Psoas Muscle	Psoas
4	chr19:37743600-37751200	Weak transcription	Left Ventricle	heart
5	chr19:37743600-37751400	Weak transcription	NHDF-Ad	bronchial
6	chr19:37743600-37752800	Weak transcription	Fetal Heart	heart
7	chr19:37743800-37747200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:37743800-37747400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:37743800-37747400	Weak transcription	Brain Angular Gyrus	brain
10	chr19:37743800-37748000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:37743800-37748000	Weak transcription	Fetal Lung	lung
12	chr19:37743800-37749800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr19:37743800-37751400	Weak transcription	Fetal Brain Male	brain
14	chr19:37743800-37752200	Weak transcription	Fetal Kidney	kidney
15	chr19:37743800-37758800	Weak transcription	Brain Anterior Caudate	brain
16	chr19:37744000-37747200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr19:37744200-37748000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:37744800-37747600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:37745200-37748200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr19:37745400-37747400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:37745600-37747400	Weak transcription	Brain Hippocampus Middle	brain
22	chr19:37745600-37758800	Weak transcription	Ovary	ovary
23	chr19:37746400-37748400	ZNF genes & repeats	Adipose Nuclei	Adipose
24	chr19:37746400-37750400	Strong transcription	Brain Germinal Matrix	brain
25	chr19:37746600-37747200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:37746600-37747400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr19:37746800-37748200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:37746800-37748400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:37746800-37748400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:37746800-37748400	Strong transcription	Brain Cingulate Gyrus	brain
31	chr19:37746800-37748400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr19:37746800-37748400	Strong transcription	Fetal Muscle Leg	muscle
33	chr19:37746800-37748400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr19:37746800-37752000	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:37746800-37752000	Strong transcription	Osteobl	bone
36	chr19:37746800-37752400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:37747000-37747800	ZNF genes & repeats	Primary B cells from cord blood	blood
38	chr19:37747000-37748400	Strong transcription	Brain Substantia Nigra	brain
39	chr19:37747000-37748600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:37747000-37752200	Strong transcription	Fetal Brain Female	brain

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