Variant report

Variant	rs7981043
Chromosome Location	chr13:50194407-50194408
allele	G/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	PAX5	chr13:50194311-50194582	GM12878	blood:	n/a	n/a
2	POLR2A	chr13:50194256-50194733	GM12892	blood:	n/a	n/a
3	SP1	chr13:50194232-50194672	GM12878	blood:	n/a	n/a
4	PAX5	chr13:50194215-50194714	GM12878	blood:	n/a	n/a
5	POU2F2	chr13:50194346-50194625	GM12878	blood:	n/a	n/a
6	ZEB1	chr13:50194314-50194596	GM12878	blood:	n/a	chr13:50194481-50194490
7	ATF2	chr13:50194258-50194615	GM12878	blood:	n/a	n/a
8	RUNX3	chr13:50194219-50194650	GM12878	blood:	n/a	n/a
9	FOXM1	chr13:50194303-50194657	GM12878	blood:	n/a	n/a
10	MEF2A	chr13:50194149-50194650	GM12878	blood:	n/a	chr13:50194249-50194270 chr13:50194392-50194400 chr13:50194333-50194344
11	POLR2A	chr13:50194245-50194851	Raji	blood:	n/a	n/a
12	EBF1	chr13:50194279-50194572	GM12878	blood:	n/a	n/a
13	MAX	chr13:50194282-50194843	HepG2	liver:	n/a	chr13:50194317-50194327 chr13:50194317-50194326 chr13:50194317-50194327 chr13:50194316-50194326
14	MAX	chr13:50194314-50194624	K562	blood:	n/a	chr13:50194317-50194327 chr13:50194317-50194326 chr13:50194317-50194327 chr13:50194316-50194326
15	PML	chr13:50194221-50194780	GM12878	blood:	n/a	n/a
16	TCF12	chr13:50194320-50194579	GM12878	blood:	n/a	n/a
17	MAX	chr13:50194168-50194791	NB4	blood:	n/a	chr13:50194317-50194327 chr13:50194317-50194326 chr13:50194317-50194327 chr13:50194316-50194326
18	TBL1XR1	chr13:50194344-50194548	GM12878	blood:	n/a	n/a
19	MTA3	chr13:50194143-50194705	GM12878	blood:	n/a	n/a
20	MYC	chr13:50194173-50194708	NB4	blood:	n/a	chr13:50194317-50194327 chr13:50194317-50194326 chr13:50194317-50194327 chr13:50194316-50194326
21	CHD2	chr13:50194348-50194654	GM12878	blood:	n/a	n/a
22	EP300	chr13:50194290-50194577	GM12878	blood:	n/a	n/a
23	POLR2A	chr13:50194258-50194919	GM12892	blood:	n/a	n/a
24	NFATC1	chr13:50194220-50194576	GM12878	blood:	n/a	n/a
25	SP1	chr13:50194273-50194559	GM12878	blood:	n/a	n/a
26	EBF1	chr13:50194401-50194501	GM12878	blood:	n/a	n/a
27	TCF12	chr13:50194384-50194600	GM12878	blood:	n/a	n/a
28	MAX	chr13:50194276-50194653	GM12878	blood:	n/a	chr13:50194317-50194327 chr13:50194317-50194326 chr13:50194317-50194327 chr13:50194316-50194326
29	EP300	chr13:50194333-50194567	GM12878	blood:	n/a	n/a
30	BCL11A	chr13:50194262-50194547	GM12878	blood:	n/a	n/a
31	MXI1	chr13:50194238-50194497	GM12878	blood:	n/a	chr13:50194317-50194326
32	POLR2A	chr13:50194342-50194697	GM12878	blood:	n/a	n/a
33	POLR2A	chr13:50194286-50194605	GM12878	blood:	n/a	n/a
34	MAZ	chr13:50194306-50194831	GM12878	blood:	n/a	chr13:50194317-50194327 chr13:50194317-50194326 chr13:50194317-50194327
35	TAF1	chr13:50194237-50194549	GM12878	blood:	n/a	n/a
36	BCL11A	chr13:50194285-50194582	GM12878	blood:	n/a	n/a
37	POLR2A	chr13:50194296-50194769	GM15510	blood:	n/a	n/a
38	BCLAF1	chr13:50194272-50194572	GM12878	blood:	n/a	n/a
39	MEF2A	chr13:50194203-50194641	GM12878	blood:	n/a	chr13:50194249-50194270 chr13:50194392-50194400 chr13:50194333-50194344
40	CTCF	chr13:50194380-50194530	GM12872	blood:	n/a	n/a
41	POLR2A	chr13:50194226-50194699	GM12892	blood:	n/a	n/a
42	RUNX3	chr13:50194176-50194683	GM12878	blood:	n/a	n/a
43	MYC	chr13:50194311-50194450	K562	blood:	n/a	chr13:50194317-50194327 chr13:50194317-50194326 chr13:50194317-50194327 chr13:50194316-50194326

Variant related genes	Relation type
ENSG00000176882	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1535467	0.92[ASN][1000 genomes]
rs1925743	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2094108	0.81[EUR][1000 genomes]
rs2146144	0.81[EUR][1000 genomes]
rs2146146	0.81[EUR][1000 genomes]
rs3803185	0.92[ASN][1000 genomes]
rs3969	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315259	0.81[EUR][1000 genomes]
rs4409984	0.81[EUR][1000 genomes]
rs4415919	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4638463	0.81[EUR][1000 genomes]
rs4942854	0.84[EUR][1000 genomes]
rs4942859	0.88[EUR][1000 genomes]
rs4942860	0.88[EUR][1000 genomes]
rs7322886	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316462	0.81[EUR][1000 genomes]
rs9316463	0.81[EUR][1000 genomes]
rs9526582	0.92[ASN][1000 genomes]
rs9535267	0.96[ASN][1000 genomes]
rs9535268	0.81[EUR][1000 genomes]
rs9535270	0.83[EUR][1000 genomes]
rs9535271	0.82[EUR][1000 genomes]
rs9535275	0.82[EUR][1000 genomes]
rs9535277	0.92[ASN][1000 genomes]
rs9568284	0.84[EUR][1000 genomes]
rs9568285	0.84[EUR][1000 genomes]
rs9568286	0.84[EUR][1000 genomes]

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	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7981043	ARL11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50190600-50195800	Weak transcription	Ovary	ovary
2	chr13:50191200-50199400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr13:50191800-50194800	Enhancers	Primary hematopoietic stem cells	blood
4	chr13:50192400-50196600	Weak transcription	Fetal Lung	lung
5	chr13:50192800-50196600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr13:50193600-50195000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:50194000-50194800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr13:50194200-50194600	Active TSS	Primary B cells from peripheral blood	blood
9	chr13:50194200-50194600	Active TSS	Duodenum Mucosa	Duodenum
10	chr13:50194200-50194600	Active TSS	GM12878-XiMat	blood
11	chr13:50194200-50194800	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr13:50194200-50194800	Enhancers	Fetal Heart	heart
13	chr13:50194200-50194800	Active TSS	K562	blood
14	chr13:50194200-50194800	Active TSS	NHDF-Ad	bronchial
15	chr13:50194400-50194600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:50194400-50194600	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr13:50194400-50194600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr13:50194400-50194600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr13:50194400-50194600	Enhancers	Brain Germinal Matrix	brain
20	chr13:50194400-50194600	Enhancers	Esophagus	oesophagus
21	chr13:50194400-50194600	Enhancers	Fetal Muscle Trunk	muscle
22	chr13:50194400-50194600	Active TSS	Fetal Muscle Leg	muscle
23	chr13:50194400-50194600	Flanking Active TSS	Left Ventricle	heart
24	chr13:50194400-50194600	Genic enhancers	Lung	lung
25	chr13:50194400-50194600	Flanking Active TSS	Osteobl	bone
26	chr13:50194400-50194800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:50194400-50194800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr13:50194400-50194800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:50194400-50194800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr13:50194400-50194800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr13:50194400-50194800	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr13:50194400-50194800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr13:50194400-50194800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr13:50194400-50194800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:50194400-50194800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr13:50194400-50194800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:50194400-50194800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:50194400-50194800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr13:50194400-50194800	Active TSS	Brain Angular Gyrus	brain
40	chr13:50194400-50194800	Active TSS	Brain Cingulate Gyrus	brain
41	chr13:50194400-50194800	Active TSS	Brain Hippocampus Middle	brain
42	chr13:50194400-50194800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:50194400-50194800	Active TSS	Colonic Mucosa	Colon
44	chr13:50194400-50194800	Enhancers	Placenta	Placenta
45	chr13:50194400-50194800	Flanking Active TSS	Fetal Thymus	thymus
46	chr13:50194400-50194800	Enhancers	Gastric	stomach
47	chr13:50194400-50194800	Flanking Active TSS	Right Atrium	heart
48	chr13:50194400-50194800	Flanking Active TSS	Right Ventricle	heart
49	chr13:50194400-50194800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr13:50194400-50194800	Active TSS	Stomach Smooth Muscle	stomach

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