Variant report

Variant	rs158373
Chromosome Location	chr10:43099542-43099543
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1255367	0.80[AMR][1000 genomes]
rs158376	0.92[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs158377	1.00[YRI][hapmap]
rs158378	1.00[YRI][hapmap]
rs158382	0.91[YRI][hapmap]
rs158384	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs158385	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs158389	0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs158391	1.00[YRI][hapmap]
rs158392	0.85[CEU][hapmap];0.96[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs210219	1.00[YRI][hapmap]
rs210224	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs210232	0.80[AMR][1000 genomes]
rs210235	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs210237	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs210253	0.81[EUR][1000 genomes]
rs210258	0.85[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs210261	0.81[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs210262	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs210272	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs210278	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs210279	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs210284	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs210287	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2184238	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2484298	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs289182	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs289183	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2982229	0.80[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs504191	1.00[YRI][hapmap]
rs668169	0.82[ASN][1000 genomes]
rs668649	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv817455	chr10:42607635-43151812	Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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	40 gene(s)	inside rSNPs	diseases
3	nsv895064	chr10:42783481-43243325	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription 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	35 gene(s)	inside rSNPs	diseases
5	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	nsv469725	chr10:42965130-43178323	Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv482513	chr10:42965130-43178323	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
12	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv975036	chr10:43090222-43132879	ZNF genes & repeats Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs158373	LINC00839	cis	Esophagus Muscularis	GTEx
rs158373	LINC00839	cis	Esophagus Mucosa	GTEx
rs158373	LINC00839	cis	lung	GTEx
rs158373	CCNYL2	cis	Artery Aorta	GTEx
rs158373	LINC00839	cis	Artery Aorta	GTEx
rs158373	LINC00839	cis	Artery Tibial	GTEx
rs158373	LINC00839	cis	Nerve Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43077800-43109600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:43089600-43123600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr10:43089800-43099800	Weak transcription	Brain Angular Gyrus	brain
4	chr10:43089800-43107600	Weak transcription	HepG2	liver
5	chr10:43089800-43126000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:43089800-43133000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr10:43089800-43133000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:43089800-43133000	Weak transcription	Right Ventricle	heart
9	chr10:43090000-43119200	Weak transcription	Brain Anterior Caudate	brain
10	chr10:43090000-43119200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:43090200-43108600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:43090400-43107200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:43090400-43108000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr10:43090400-43118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:43090600-43104800	Weak transcription	Hela-S3	cervix
16	chr10:43090600-43107200	Weak transcription	K562	blood
17	chr10:43090800-43133000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr10:43091000-43123800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:43091200-43100200	Weak transcription	Fetal Brain Male	brain
20	chr10:43091200-43107800	Weak transcription	Fetal Thymus	thymus
21	chr10:43091200-43108800	Weak transcription	Adipose Nuclei	Adipose
22	chr10:43091200-43123600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr10:43091200-43126000	Weak transcription	Small Intestine	intestine
24	chr10:43091200-43132800	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:43091400-43101200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:43091400-43101200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr10:43091400-43101400	Weak transcription	Ovary	ovary
28	chr10:43091400-43107600	Weak transcription	Psoas Muscle	Psoas
29	chr10:43091400-43108400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr10:43091400-43119600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr10:43091400-43132400	Weak transcription	HMEC	breast
32	chr10:43091400-43132800	Weak transcription	Colonic Mucosa	Colon
33	chr10:43091800-43107800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr10:43093800-43100200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr10:43094000-43100000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr10:43094000-43108400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr10:43094000-43108600	Weak transcription	Fetal Muscle Leg	muscle
38	chr10:43094000-43119400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr10:43094000-43119400	Weak transcription	Spleen	Spleen
40	chr10:43094200-43100000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:43094200-43100600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:43094200-43105200	Weak transcription	Fetal Kidney	kidney
43	chr10:43094200-43107600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr10:43094200-43119400	Weak transcription	Right Atrium	heart
45	chr10:43094400-43103600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr10:43094400-43133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr10:43095200-43103000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr10:43095400-43126000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr10:43095600-43125800	Weak transcription	HUVEC	blood vessel
50	chr10:43095800-43102200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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