Variant report

Variant	rs1147919
Chromosome Location	chr10:43091958-43091959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr10:43091708-43091999	K562	blood:	n/a	n/a
2	MAFK	chr10:43091709-43092036	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000272373	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1147916	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1147917	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1147918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255369	0.86[AFR][1000 genomes]
rs1255370	0.86[AFR][1000 genomes]
rs1255385	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1255386	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1255387	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1255392	0.81[AFR][1000 genomes]
rs1255395	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1255396	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1255414	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs209394	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2473112	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473115	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2473116	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2484296	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2504025	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1147919	LINC00839	cis	lung	GTEx
rs1147919	LINC00839	cis	Artery Aorta	GTEx
rs1147919	LINC00839	cis	Esophagus Muscularis	GTEx
rs1147919	RP11-313J2.1	cis	Nerve Tibial	GTEx
rs1147919	LINC00839	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43077800-43109600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:43081800-43092000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
3	chr10:43082000-43092200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:43082200-43092600	ZNF genes & repeats	Liver	Liver
5	chr10:43083000-43094800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
6	chr10:43084800-43092600	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr10:43085000-43092400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:43085200-43096400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr10:43085600-43092400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:43086400-43092000	ZNF genes & repeats	Primary B cells from cord blood	blood
11	chr10:43086400-43094000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:43087000-43097000	Weak transcription	Fetal Stomach	stomach
13	chr10:43089400-43093800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:43089600-43093600	Weak transcription	Gastric	stomach
15	chr10:43089600-43123600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr10:43089800-43092200	Weak transcription	Fetal Heart	heart
17	chr10:43089800-43093000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr10:43089800-43098400	Weak transcription	Thymus	Thymus
19	chr10:43089800-43099800	Weak transcription	Brain Angular Gyrus	brain
20	chr10:43089800-43107600	Weak transcription	HepG2	liver
21	chr10:43089800-43126000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:43089800-43133000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr10:43089800-43133000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr10:43089800-43133000	Weak transcription	Right Ventricle	heart
25	chr10:43090000-43119200	Weak transcription	Brain Anterior Caudate	brain
26	chr10:43090000-43119200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr10:43090200-43108600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:43090400-43099200	Weak transcription	Placenta	Placenta
29	chr10:43090400-43107200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr10:43090400-43108000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr10:43090400-43118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr10:43090600-43104800	Weak transcription	Hela-S3	cervix
33	chr10:43090600-43107200	Weak transcription	K562	blood
34	chr10:43090800-43096200	Weak transcription	Brain Hippocampus Middle	brain
35	chr10:43090800-43133000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr10:43091000-43123800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:43091200-43092400	Weak transcription	A549	lung
38	chr10:43091200-43093600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:43091200-43093600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr10:43091200-43093600	Weak transcription	Pancreas	Pancrea
41	chr10:43091200-43093800	Weak transcription	Fetal Kidney	kidney
42	chr10:43091200-43094200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr10:43091200-43096200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr10:43091200-43098800	Weak transcription	Brain Germinal Matrix	brain
45	chr10:43091200-43100200	Weak transcription	Fetal Brain Male	brain
46	chr10:43091200-43107800	Weak transcription	Fetal Thymus	thymus
47	chr10:43091200-43108800	Weak transcription	Adipose Nuclei	Adipose
48	chr10:43091200-43123600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr10:43091200-43126000	Weak transcription	Small Intestine	intestine
50	chr10:43091200-43132800	Weak transcription	Colon Smooth Muscle	Colon

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