Variant report

Variant	rs210258
Chromosome Location	chr10:43034123-43034124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1255366	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1255367	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1255368	0.88[EUR][1000 genomes]
rs1255371	0.87[EUR][1000 genomes]
rs1255372	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1255403	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255405	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1255407	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1255412	0.81[ASN][1000 genomes]
rs158373	0.85[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs158376	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs158377	1.00[YRI][hapmap]
rs158378	1.00[YRI][hapmap]
rs158382	0.91[YRI][hapmap]
rs158391	1.00[YRI][hapmap]
rs158392	0.85[CEU][hapmap]
rs1760687	0.90[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs210219	1.00[YRI][hapmap]
rs210224	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs210232	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs210233	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210235	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210237	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs210242	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs210253	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210261	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210262	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210272	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs210278	0.80[EUR][1000 genomes]
rs210279	0.82[AMR][1000 genomes]
rs210284	0.92[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs210287	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2484298	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2801951	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs289183	0.84[CEU][hapmap]
rs2982229	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs504191	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv550670	chr10:42725663-43089965	Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	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
4	nsv895054	chr10:42761931-43068841	ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	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
6	nsv466877	chr10:42794125-43066414	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv550683	chr10:42794125-43066414	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv895071	chr10:42864138-43066414	ZNF genes & repeats Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv895073	chr10:42884169-43066505	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs210258	LINC00839	cis	Esophagus Muscularis	GTEx
rs210258	LINC00839	cis	Nerve Tibial	GTEx
rs210258	LINC00839	cis	Artery Tibial	GTEx
rs210258	LINC00839	cis	Artery Aorta	GTEx
rs210258	CCNYL2	cis	Artery Aorta	GTEx
rs210258	LINC00839	cis	Esophagus Mucosa	GTEx
rs210258	LINC00839	cis	lung	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43019600-43034400	Weak transcription	Fetal Thymus	thymus
2	chr10:43020400-43047000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr10:43020600-43039200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:43020600-43047000	Weak transcription	HSMM	muscle
5	chr10:43020800-43034200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:43021600-43047000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:43029000-43034800	Weak transcription	K562	blood
8	chr10:43029600-43034600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:43030600-43034200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr10:43031600-43034600	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:43031800-43034800	Weak transcription	Left Ventricle	heart
12	chr10:43032000-43034800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:43032000-43034800	Weak transcription	Brain Anterior Caudate	brain
14	chr10:43032600-43034600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:43032600-43034600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr10:43032600-43035000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:43032800-43034400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:43032800-43034600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:43032800-43034600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr10:43032800-43035200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:43033200-43034400	Weak transcription	Liver	Liver
22	chr10:43033400-43034800	Weak transcription	Fetal Lung	lung
23	chr10:43033600-43034200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr10:43033600-43034400	Weak transcription	Pancreas	Pancrea
25	chr10:43033600-43035200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:43033800-43034600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:43033800-43034800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr10:43033800-43035400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr10:43033800-43035400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr10:43033800-43035600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
31	chr10:43033800-43035800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
32	chr10:43033800-43035800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:43033800-43036200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
34	chr10:43033800-43037600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr10:43033800-43041400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:43034000-43034600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr10:43034000-43035000	Weak transcription	Brain Angular Gyrus	brain
38	chr10:43034000-43035000	Weak transcription	GM12878-XiMat	blood
39	chr10:43034000-43035600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:43034000-43035600	ZNF genes & repeats	Adipose Nuclei	Adipose
41	chr10:43034000-43035600	ZNF genes & repeats	Brain Germinal Matrix	brain
42	chr10:43034000-43035600	ZNF genes & repeats	Ovary	ovary
43	chr10:43034000-43035800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:43034000-43035800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
45	chr10:43034000-43035800	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr10:43034000-43036200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:43034000-43036800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:43034000-43036800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:43034000-43037800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
50	chr10:43034000-43039200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--

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