Variant report

Variant	rs9535274
Chromosome Location	chr13:50194394-50194395
allele	A/G
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	TCF12	chr13:50194384-50194600	GM12878	blood:	n/a	n/a
27	MAX	chr13:50194276-50194653	GM12878	blood:	n/a	chr13:50194317-50194327 chr13:50194317-50194326 chr13:50194317-50194327 chr13:50194316-50194326
28	EP300	chr13:50194333-50194567	GM12878	blood:	n/a	n/a
29	BCL11A	chr13:50194262-50194547	GM12878	blood:	n/a	n/a
30	MXI1	chr13:50194238-50194497	GM12878	blood:	n/a	chr13:50194317-50194326
31	POLR2A	chr13:50194342-50194697	GM12878	blood:	n/a	n/a
32	POLR2A	chr13:50194286-50194605	GM12878	blood:	n/a	n/a
33	MAZ	chr13:50194306-50194831	GM12878	blood:	n/a	chr13:50194317-50194327 chr13:50194317-50194326 chr13:50194317-50194327
34	TAF1	chr13:50194237-50194549	GM12878	blood:	n/a	n/a
35	BCL11A	chr13:50194285-50194582	GM12878	blood:	n/a	n/a
36	POLR2A	chr13:50194296-50194769	GM15510	blood:	n/a	n/a
37	BCLAF1	chr13:50194272-50194572	GM12878	blood:	n/a	n/a
38	MEF2A	chr13:50194203-50194641	GM12878	blood:	n/a	chr13:50194249-50194270 chr13:50194392-50194400 chr13:50194333-50194344
39	CTCF	chr13:50194380-50194530	GM12872	blood:	n/a	n/a
40	POLR2A	chr13:50194226-50194699	GM12892	blood:	n/a	n/a
41	RUNX3	chr13:50194176-50194683	GM12878	blood:	n/a	n/a
42	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: 11 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4942855	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7326010	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526581	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9535274	ARL11	Cis_1M	lymphoblastoid	RTeQTL
rs9535274	ARL11	cis	lymphoblastoid	GTEx
rs9535274	RCBTB1	cis	parietal	SCAN
rs9535274	ARL11	cis	lymphoblastoid	seeQTL
rs9535274	RCBTB1	cis	cerebellum	SCAN
rs9535274	CDADC1	cis	cerebellum	SCAN
rs9535274	CAB39L	cis	cerebellum	SCAN
rs9535274	NXF3	trans	cerebellum	SCAN
rs9535274	ARL11	cis	multi-tissue	Pritchard
rs9535274	ESD	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50181400-50194400	Weak transcription	Right Ventricle	heart
2	chr13:50190200-50194400	Weak transcription	Left Ventricle	heart
3	chr13:50190200-50194400	Weak transcription	Spleen	Spleen
4	chr13:50190400-50194400	Weak transcription	Brain Angular Gyrus	brain
5	chr13:50190400-50194400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr13:50190600-50194400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr13:50190600-50195800	Weak transcription	Ovary	ovary
8	chr13:50190800-50194400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:50190800-50194400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:50190800-50194400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr13:50191000-50194400	Weak transcription	Brain Germinal Matrix	brain
12	chr13:50191200-50194400	Weak transcription	Adipose Nuclei	Adipose
13	chr13:50191200-50199400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr13:50191400-50194400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr13:50191400-50194400	Enhancers	Fetal Thymus	thymus
16	chr13:50191600-50194400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr13:50191800-50194800	Enhancers	Primary hematopoietic stem cells	blood
18	chr13:50192000-50194400	Enhancers	Primary B cells from cord blood	blood
19	chr13:50192400-50194400	Weak transcription	Lung	lung
20	chr13:50192400-50196600	Weak transcription	Fetal Lung	lung
21	chr13:50192800-50196600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr13:50193200-50194400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr13:50193400-50194400	Weak transcription	Fetal Muscle Leg	muscle
24	chr13:50193600-50195000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr13:50194000-50194800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr13:50194200-50194400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr13:50194200-50194400	Active TSS	Primary T cells from cord blood	blood
28	chr13:50194200-50194400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr13:50194200-50194400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr13:50194200-50194400	Active TSS	Right Atrium	heart
31	chr13:50194200-50194400	Active TSS	Thymus	Thymus
32	chr13:50194200-50194600	Active TSS	Primary B cells from peripheral blood	blood
33	chr13:50194200-50194600	Active TSS	Duodenum Mucosa	Duodenum
34	chr13:50194200-50194600	Active TSS	GM12878-XiMat	blood
35	chr13:50194200-50194800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr13:50194200-50194800	Enhancers	Fetal Heart	heart
37	chr13:50194200-50194800	Active TSS	K562	blood
38	chr13:50194200-50194800	Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links