Variant report

Variant	rs689319
Chromosome Location	chr18:8144269-8144270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11081360	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11660158	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11663160	0.80[EUR][1000 genomes]
rs11872382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16952967	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17398368	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17476745	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526853	1.00[CHB][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv458018	chr18:8110805-8645907	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv576426	chr18:8110805-8645907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs689319	LAMA1	cis	cerebellum	SCAN
rs689319	NAPG	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8117400-8153200	Weak transcription	Liver	Liver
2	chr18:8121200-8145600	Weak transcription	Primary T cells from cord blood	blood
3	chr18:8122400-8157400	Weak transcription	Aorta	Aorta
4	chr18:8122400-8160400	Weak transcription	Thymus	Thymus
5	chr18:8126800-8153200	Weak transcription	A549	lung
6	chr18:8137400-8153400	Weak transcription	Placenta	Placenta
7	chr18:8139000-8158800	Weak transcription	Pancreas	Pancrea
8	chr18:8139600-8151000	Weak transcription	Fetal Stomach	stomach
9	chr18:8139800-8147000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr18:8140000-8153200	Weak transcription	Fetal Heart	heart
11	chr18:8140200-8145400	Weak transcription	Fetal Muscle Leg	muscle
12	chr18:8140200-8146800	Weak transcription	Fetal Brain Male	brain
13	chr18:8141400-8144400	Weak transcription	Fetal Thymus	thymus
14	chr18:8141400-8150800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr18:8141600-8148200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr18:8141600-8151000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr18:8141600-8159200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr18:8142200-8156000	Weak transcription	HepG2	liver
19	chr18:8142400-8157800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr18:8142600-8147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr18:8142600-8151400	Weak transcription	Ovary	ovary
22	chr18:8142600-8153600	Weak transcription	HSMM	muscle
23	chr18:8142600-8160200	Weak transcription	Psoas Muscle	Psoas
24	chr18:8142600-8162400	Weak transcription	Right Ventricle	heart
25	chr18:8142800-8145600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr18:8142800-8151000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr18:8143000-8153800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr18:8143200-8144400	Weak transcription	Adipose Nuclei	Adipose
29	chr18:8143200-8145400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:8143200-8153200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr18:8143600-8144600	Strong transcription	Lung	lung
32	chr18:8143600-8145600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr18:8143600-8146000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr18:8143600-8147000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr18:8143800-8144600	Strong transcription	Fetal Lung	lung
36	chr18:8143800-8144800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr18:8144000-8144400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr18:8144000-8145400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:8144000-8145600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr18:8144000-8146000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr18:8144200-8144400	Strong transcription	Left Ventricle	heart
42	chr18:8144200-8144600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr18:8144200-8145000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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