Variant report

Variant	rs9568289
Chromosome Location	chr13:50199211-50199212
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	RAD21	chr13:50199179-50199437	HepG2	liver:	n/a	n/a
2	CTCF	chr13:50199163-50199411	HepG2	liver:	n/a	n/a
3	MAX	chr13:50199110-50200397	HepG2	liver:	n/a	chr13:50199685-50199695
4	RCOR1	chr13:50199122-50199264	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50198466..50201359-chr13:50202667..50205096,2	MCF-7	breast:
2	chr13:50016671..50019335-chr13:50197753..50200555,2	K562	blood:

Variant related genes	Relation type
ARL11	TF binding region
ENSG00000136169	Chromatin interaction
ENSG00000102547	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11616980	0.82[ASN][1000 genomes]
rs11618686	0.82[ASN][1000 genomes]
rs1830629	0.89[EUR][1000 genomes]
rs2407793	0.90[EUR][1000 genomes]
rs2407794	0.90[EUR][1000 genomes]
rs2897768	0.90[EUR][1000 genomes]
rs4344626	0.90[EUR][1000 genomes]
rs4595700	0.90[EUR][1000 genomes]
rs6561546	0.90[EUR][1000 genomes]
rs6561547	0.90[EUR][1000 genomes]
rs6561548	0.84[EUR][1000 genomes]
rs6561549	0.82[EUR][1000 genomes]
rs7327293	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7331252	0.90[EUR][1000 genomes]
rs7332484	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7332771	0.90[EUR][1000 genomes]
rs9568270	0.88[EUR][1000 genomes]
rs9568272	0.89[EUR][1000 genomes]
rs9568274	0.80[ASN][1000 genomes]
rs9568275	0.89[EUR][1000 genomes]
rs9568276	0.88[EUR][1000 genomes]
rs9568277	0.89[EUR][1000 genomes]
rs9568279	0.90[EUR][1000 genomes]
rs9568280	0.89[EUR][1000 genomes]
rs9568281	0.80[ASN][1000 genomes]
rs9568282	0.90[EUR][1000 genomes]
rs9568283	0.90[EUR][1000 genomes]
rs9568288	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596159	0.89[EUR][1000 genomes]
rs9596160	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
7	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9568289	RCBTB1	cis	Whole Blood	GTEx
rs9568289	KPNA3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50191200-50199400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:50194600-50202000	Weak transcription	Esophagus	oesophagus
3	chr13:50194800-50199600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:50194800-50199600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:50194800-50199600	Weak transcription	Gastric	stomach
6	chr13:50194800-50199600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr13:50194800-50200000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:50194800-50201800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr13:50194800-50202000	Weak transcription	Primary B cells from cord blood	blood
10	chr13:50194800-50202000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr13:50194800-50202000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr13:50194800-50202000	Weak transcription	Fetal Thymus	thymus
13	chr13:50194800-50202000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:50194800-50202200	Weak transcription	Colonic Mucosa	Colon
15	chr13:50194800-50202200	Weak transcription	K562	blood
16	chr13:50195800-50200400	Enhancers	Fetal Heart	heart
17	chr13:50196800-50199600	Weak transcription	Left Ventricle	heart
18	chr13:50196800-50199600	Weak transcription	Right Atrium	heart
19	chr13:50197000-50199400	Weak transcription	Adipose Nuclei	Adipose
20	chr13:50197000-50199600	Weak transcription	Fetal Lung	lung
21	chr13:50197000-50199600	Weak transcription	Ovary	ovary
22	chr13:50197000-50201800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:50198600-50200400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr13:50198800-50200200	Enhancers	Lung	lung
25	chr13:50198800-50200400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr13:50198800-50200400	Enhancers	Spleen	Spleen
27	chr13:50199000-50199800	Enhancers	Liver	Liver
28	chr13:50199000-50201400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr13:50199200-50199600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:50199200-50199600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr13:50199200-50199600	Weak transcription	Brain Hippocampus Middle	brain
32	chr13:50199200-50199800	Enhancers	Duodenum Mucosa	Duodenum
33	chr13:50199200-50200000	Enhancers	Right Ventricle	heart
34	chr13:50199200-50200000	Flanking Active TSS	Hela-S3	cervix
35	chr13:50199200-50200200	Enhancers	Placenta	Placenta
36	chr13:50199200-50200400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:50199200-50200400	Enhancers	Fetal Intestine Large	intestine
38	chr13:50199200-50200800	Flanking Active TSS	HepG2	liver

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