Variant report

Variant	rs616019
Chromosome Location	chr18:7743140-7743141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1664980	0.83[EUR][1000 genomes]
rs1664981	0.82[EUR][1000 genomes]
rs17473649	1.00[CHB][hapmap]
rs1940344	0.80[EUR][1000 genomes]
rs4121619	1.00[CHD][hapmap];0.84[GIH][hapmap]
rs422656	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4797301	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs4798586	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs4798590	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs582641	0.80[EUR][1000 genomes]
rs582683	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs587215	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs587368	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs589371	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs597736	0.92[CEU][hapmap]
rs598136	0.80[EUR][1000 genomes]
rs599006	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599960	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs605077	0.80[EUR][1000 genomes]
rs608028	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs613706	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs624519	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs626015	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs629562	0.81[CEU][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs640128	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap]
rs644399	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs649301	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap]
rs658744	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs658864	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs661828	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs664592	0.96[CEU][hapmap];0.85[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs677083	0.80[EUR][1000 genomes]
rs677443	0.80[EUR][1000 genomes]
rs678492	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs679539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679873	0.81[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs689014	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap]
rs7236295	1.00[CHB][hapmap]
rs9953589	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064597	chr18:7169490-7762738	Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv543636	chr18:7169490-7762738	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv458017	chr18:7689201-7747873	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv576420	chr18:7689201-7747873	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv470406	chr18:7700462-7747873	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1064869	chr18:7730116-7760969	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1061538	chr18:7730116-7762149	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv1067394	chr18:7730116-7768536	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv2656311	chr18:7732141-7761056	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1057760	chr18:7732188-7760969	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv431970	chr18:7732188-7770950	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv525328	chr18:7732917-7760498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv576421	chr18:7732917-7761056	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv576422	chr18:7732917-7763363	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv576423	chr18:7732917-7788329	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv576424	chr18:7740473-7761056	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs616019	VAPA	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7734600-7745600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr18:7735200-7745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:7735400-7745200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr18:7735800-7745200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr18:7736200-7745000	Weak transcription	A549	lung
6	chr18:7737800-7746800	Weak transcription	Spleen	Spleen
7	chr18:7737800-7748400	Weak transcription	Gastric	stomach
8	chr18:7738000-7746600	Weak transcription	Right Atrium	heart
9	chr18:7739000-7746800	Weak transcription	Pancreas	Pancrea
10	chr18:7739000-7750600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr18:7739600-7743200	Enhancers	Fetal Muscle Leg	muscle
12	chr18:7740800-7743400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr18:7740800-7744000	Enhancers	Adipose Nuclei	Adipose
14	chr18:7741000-7744000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr18:7741200-7743200	Enhancers	Left Ventricle	heart
16	chr18:7741200-7743200	Enhancers	Psoas Muscle	Psoas
17	chr18:7741200-7743400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr18:7741200-7743400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr18:7741200-7744400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr18:7741400-7743200	Enhancers	Colon Smooth Muscle	Colon
21	chr18:7741400-7745200	Weak transcription	Aorta	Aorta
22	chr18:7741400-7746800	Weak transcription	Right Ventricle	heart
23	chr18:7741600-7745400	Weak transcription	Fetal Kidney	kidney
24	chr18:7741600-7747400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr18:7741800-7743200	Enhancers	NHDF-Ad	bronchial
26	chr18:7742000-7744000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr18:7742000-7744000	Weak transcription	Brain Anterior Caudate	brain
28	chr18:7742000-7744200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr18:7742000-7745600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr18:7742000-7747800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr18:7742000-7748200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr18:7742000-7751400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr18:7742600-7743200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr18:7742600-7743400	Enhancers	Fetal Lung	lung
35	chr18:7742600-7745400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr18:7742800-7748400	Weak transcription	Fetal Stomach	stomach
37	chr18:7743000-7743200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:7743000-7743200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr18:7743000-7743400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr18:7743000-7743400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr18:7743000-7743400	Enhancers	Fetal Heart	heart

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