Variant report

Variant	rs2504025
Chromosome Location	chr10:43118592-43118593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43117987..43119572-chr10:43133263..43135094,2	K562	blood:

Variant related genes	Relation type
ENSG00000196693	Chromatin interaction
ENSG00000272373	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1147916	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1147917	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1147918	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1147919	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255369	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1255370	0.86[AFR][1000 genomes]
rs1255385	0.80[AMR][1000 genomes]
rs1255386	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1255387	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1255392	0.81[AFR][1000 genomes]
rs1255395	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1255396	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1255414	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs209394	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2473112	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2473115	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2473116	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2484296	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
14	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2504025	LINC00839	cis	Artery Aorta	GTEx
rs2504025	LINC00839	cis	Artery Tibial	GTEx
rs2504025	LINC00839	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43089600-43123600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr10:43089800-43126000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:43089800-43133000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr10:43089800-43133000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:43089800-43133000	Weak transcription	Right Ventricle	heart
6	chr10:43090000-43119200	Weak transcription	Brain Anterior Caudate	brain
7	chr10:43090000-43119200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:43090400-43118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr10:43090800-43133000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:43091000-43123800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr10:43091200-43123600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr10:43091200-43126000	Weak transcription	Small Intestine	intestine
13	chr10:43091200-43132800	Weak transcription	Colon Smooth Muscle	Colon
14	chr10:43091400-43119600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr10:43091400-43132400	Weak transcription	HMEC	breast
16	chr10:43091400-43132800	Weak transcription	Colonic Mucosa	Colon
17	chr10:43094000-43119400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:43094000-43119400	Weak transcription	Spleen	Spleen
19	chr10:43094200-43119400	Weak transcription	Right Atrium	heart
20	chr10:43094400-43133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:43095400-43126000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr10:43095600-43125800	Weak transcription	HUVEC	blood vessel
23	chr10:43096800-43119400	Weak transcription	NHEK	skin
24	chr10:43101000-43133000	Weak transcription	NH-A	brain
25	chr10:43102000-43119400	Weak transcription	Gastric	stomach
26	chr10:43102000-43126200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:43102000-43132000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr10:43105800-43119400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr10:43106200-43132600	Weak transcription	Fetal Heart	heart
30	chr10:43107000-43133000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr10:43107400-43129000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr10:43107800-43119400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr10:43108000-43133200	Weak transcription	Psoas Muscle	Psoas
34	chr10:43108800-43119400	Weak transcription	Left Ventricle	heart
35	chr10:43109000-43133200	Weak transcription	Aorta	Aorta
36	chr10:43109400-43119000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr10:43109600-43118600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr10:43109600-43118800	Weak transcription	Brain Germinal Matrix	brain
39	chr10:43109600-43119200	Weak transcription	Fetal Kidney	kidney
40	chr10:43109600-43119400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr10:43109600-43119400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr10:43109600-43119400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:43109600-43119400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:43109600-43119400	Weak transcription	Fetal Stomach	stomach
45	chr10:43109800-43118800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr10:43109800-43119400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr10:43109800-43126000	Weak transcription	Fetal Brain Male	brain
48	chr10:43109800-43126000	Weak transcription	Fetal Muscle Leg	muscle
49	chr10:43110000-43118800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr10:43110000-43118800	Weak transcription	K562	blood

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