Variant report

Variant	rs1800623
Chromosome Location	chr10:90776083-90776084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAS-1	chr10:90775593-90776816	ENSG00000261438.1

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10509561	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10887879	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202925	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202927	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12257092	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810764	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926188	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011806	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031611	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031613	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147419	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2234978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4064	1.00[JPT][hapmap]
rs4934435	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4934436	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7089946	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7092857	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916294	1.00[JPT][hapmap]

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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1800623	ACTA2	Cis_1M	lymphoblastoid	RTeQTL
rs1800623	GRID1	cis	parietal	SCAN
rs1800623	FAS	cis	parietal	SCAN
rs1800623	LIPK	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90754000-90779400	Weak transcription	HepG2	liver
2	chr10:90754000-90789600	Weak transcription	A549	lung
3	chr10:90755600-90776200	Weak transcription	Pancreas	Pancrea
4	chr10:90756200-90781800	Weak transcription	Stomach Mucosa	stomach
5	chr10:90760400-90780400	Weak transcription	Brain Angular Gyrus	brain
6	chr10:90761600-90779000	Weak transcription	Dnd41	blood
7	chr10:90761600-90779400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr10:90761800-90776200	Weak transcription	Right Ventricle	heart
9	chr10:90761800-90779600	Weak transcription	HSMMtube	muscle
10	chr10:90761800-90779800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr10:90761800-90783800	Weak transcription	Gastric	stomach
12	chr10:90761800-90786200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr10:90762400-90785800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:90762600-90777400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr10:90762600-90779400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr10:90762600-90780400	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:90762600-90786000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:90762800-90778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr10:90762800-90781000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr10:90762800-90782000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr10:90763000-90779600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr10:90763400-90777600	Strong transcription	NHDF-Ad	bronchial
23	chr10:90763600-90780800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr10:90766000-90780400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr10:90766200-90785600	Strong transcription	GM12878-XiMat	blood
26	chr10:90766800-90776600	Strong transcription	HMEC	breast
27	chr10:90767200-90776800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr10:90767200-90778000	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr10:90767400-90778000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:90767400-90779000	Strong transcription	Liver	Liver
31	chr10:90767400-90781000	Strong transcription	Osteobl	bone
32	chr10:90767600-90776800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr10:90767600-90778800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:90767600-90780800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr10:90767600-90786600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr10:90767800-90777400	Weak transcription	Fetal Intestine Small	intestine
37	chr10:90767800-90779600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr10:90767800-90781800	Weak transcription	Small Intestine	intestine
39	chr10:90768000-90776200	Strong transcription	HSMM	muscle
40	chr10:90768400-90776200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr10:90768400-90780000	Weak transcription	Psoas Muscle	Psoas
42	chr10:90768400-90785000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr10:90768800-90779200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr10:90769200-90779600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr10:90769400-90781400	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr10:90771600-90776800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr10:90771600-90779400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr10:90771600-90782600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr10:90771600-90784800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr10:90771600-90789600	Weak transcription	Brain Anterior Caudate	brain

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