Variant report

Variant	rs10793620
Chromosome Location	chr10:46087283-46087284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10466245	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs10793619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10900218	0.84[ASN][1000 genomes]
rs10900219	0.84[ASN][1000 genomes]
rs10900220	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900221	0.85[GIH][hapmap]
rs10900222	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10900223	0.84[CEU][hapmap]
rs11239535	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11239537	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239545	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs11239548	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239550	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239571	0.88[GIH][hapmap]
rs11499089	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12265787	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12269352	0.92[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12767823	0.84[ASN][1000 genomes]
rs1982796	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34563674	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57491883	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7086046	0.81[CEU][hapmap];0.88[GIH][hapmap]
rs7089063	0.84[ASN][1000 genomes]
rs7908745	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs963029	0.84[ASN][1000 genomes]
rs964686	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs970548	0.81[CEU][hapmap];0.88[GIH][hapmap]

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	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1041417	chr10:46021181-46088061	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1052233	chr10:46024620-46088061	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2761592	chr10:46072872-46090202	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10793620	MARCH8	cis	cerebellum	SCAN
rs10793620	ZNF485	cis	parietal	SCAN
rs10793620	ALOX5	cis	cerebellum	SCAN
rs10793620	ALOX5	cis	parietal	SCAN
rs10793620	ZNF32	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46076800-46087800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr10:46076800-46087800	Weak transcription	Brain Angular Gyrus	brain
3	chr10:46076800-46088000	Weak transcription	Colonic Mucosa	Colon
4	chr10:46076800-46088000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:46076800-46089000	Weak transcription	Right Ventricle	heart
6	chr10:46077400-46087800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr10:46077400-46087800	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:46077600-46087400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr10:46077600-46088400	Weak transcription	Osteobl	bone
10	chr10:46077800-46087400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:46077800-46087800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:46077800-46088400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr10:46077800-46088400	Weak transcription	NHLF	lung
14	chr10:46078200-46088000	Weak transcription	Fetal Intestine Large	intestine
15	chr10:46080200-46088000	Weak transcription	Hela-S3	cervix
16	chr10:46080400-46088800	Weak transcription	A549	lung
17	chr10:46081600-46089000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr10:46082400-46088200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:46082800-46088400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:46083400-46088800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr10:46083400-46088800	Weak transcription	Aorta	Aorta
22	chr10:46084000-46088400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:46084000-46088800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:46084000-46088800	Weak transcription	Fetal Intestine Small	intestine
25	chr10:46084400-46088400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr10:46084400-46088800	Weak transcription	Fetal Stomach	stomach
27	chr10:46084800-46088000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr10:46084800-46088400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr10:46084800-46088600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:46085400-46088000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr10:46085400-46089400	Weak transcription	Placenta	Placenta
32	chr10:46085600-46088000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:46085600-46088000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr10:46085800-46087800	Weak transcription	Adipose Nuclei	Adipose
35	chr10:46085800-46088000	Weak transcription	Brain Anterior Caudate	brain
36	chr10:46085800-46088400	Weak transcription	Fetal Brain Female	brain
37	chr10:46085800-46088800	Weak transcription	Fetal Kidney	kidney
38	chr10:46086000-46087800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:46086000-46087800	Weak transcription	Primary T cells from cord blood	blood
40	chr10:46086000-46088000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr10:46086000-46088000	Weak transcription	Fetal Lung	lung
42	chr10:46086000-46088400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr10:46086000-46088600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:46086000-46088800	Weak transcription	HSMMtube	muscle
45	chr10:46086000-46089000	Weak transcription	Fetal Muscle Leg	muscle
46	chr10:46086000-46089200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:46086200-46089000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr10:46086400-46087400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr10:46086400-46088400	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr10:46086400-46089000	Weak transcription	Pancreas	Pancrea

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