Variant report

Variant	rs201789
Chromosome Location	chr13:50986118-50986119
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	FOSL1	chr13:50985024-50986142	HCT-116	colon:	n/a	chr13:50985752-50985763 chr13:50985755-50985764 chr13:50985754-50985765
2	TCF12	chr13:50986060-50986845	SK-N-SH	brain:	n/a	n/a
3	TCF7L2	chr13:50985417-50986127	PANC-1	pancreas:	n/a	chr13:50985756-50985765 chr13:50985755-50985764
4	TCF12	chr13:50985103-50986835	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr13:50985148-50986671	SK-N-SH	brain:	n/a	chr13:50985938-50985945
6	JUND	chr13:50985101-50986819	SK-N-SH	brain:	n/a	chr13:50985752-50985763 chr13:50985493-50985504 chr13:50985755-50985764
7	JUN	chr13:50985259-50986118	K562	blood:	n/a	chr13:50985752-50985763 chr13:50985755-50985764
8	TEAD4	chr13:50985214-50986142	SK-N-SH	brain:	n/a	n/a
9	NFIC	chr13:50984957-50986737	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:50984955..50986600-chr13:50990801..50992508,2	K562	blood:
2	chr13:50965613..50967584-chr13:50985177..50987137,2	K562	blood:
3	chr13:50984531..50986156-chr13:50996985..50999573,2	K562	blood:
4	chr13:50973047..50975458-chr13:50984345..50987088,2	K562	blood:

Variant related genes	Relation type
DLEU1	TF binding region
ENSG00000176124	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1262872	0.85[ASN][1000 genomes]
rs1410113	0.83[JPT][hapmap]
rs149846	1.00[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17074346	0.83[ASN][1000 genomes]
rs201763	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201767	0.81[ASN][1000 genomes]
rs201768	0.81[ASN][1000 genomes]
rs201772	0.84[ASN][1000 genomes]
rs201777	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201778	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs201781	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201782	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201783	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201784	0.91[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201786	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201796	0.80[ASN][1000 genomes]
rs201798	0.80[ASN][1000 genomes]
rs201807	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs719103	0.81[CHB][hapmap]
rs7334326	0.84[ASN][1000 genomes]
rs9316495	0.92[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9568405	1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs9568416	0.81[ASN][1000 genomes]
rs9568433	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832609	chr13:50946577-51065968	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1045237	chr13:50976560-51102386	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Anthropometric traits	19260139	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs201789	ITM2B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50968200-50986600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr13:50975400-50996200	Weak transcription	Right Ventricle	heart
3	chr13:50980200-50987800	Enhancers	Thymus	Thymus
4	chr13:50980800-50988200	Enhancers	Fetal Thymus	thymus
5	chr13:50981200-50993000	Weak transcription	Fetal Heart	heart
6	chr13:50982400-50987200	Weak transcription	Aorta	Aorta
7	chr13:50983600-50986200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr13:50983600-50987400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:50984400-50986400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:50984400-50987200	Enhancers	HUVEC	blood vessel
11	chr13:50984800-50986800	Enhancers	HMEC	breast
12	chr13:50984800-50987400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:50984800-50987400	Enhancers	HSMMtube	muscle
14	chr13:50984800-50987800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:50984800-50987800	Enhancers	HSMM	muscle
16	chr13:50984800-50988000	Enhancers	Dnd41	blood
17	chr13:50985000-50986600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr13:50985000-50986800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:50985000-50986800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:50985000-50986800	Enhancers	NHEK	skin
21	chr13:50985000-50987200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:50985000-50987200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:50985000-50987200	Enhancers	Fetal Lung	lung
24	chr13:50985000-50987400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr13:50985000-50987400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr13:50985000-50987400	Enhancers	NHLF	lung
27	chr13:50985000-50987600	Enhancers	Fetal Stomach	stomach
28	chr13:50985000-50987600	Enhancers	NH-A	brain
29	chr13:50985000-50987800	Enhancers	NHDF-Ad	bronchial
30	chr13:50985000-50987800	Enhancers	Osteobl	bone
31	chr13:50985200-50986200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr13:50985200-50986400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr13:50985200-50987200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr13:50985200-50988000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:50985400-50986800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr13:50985400-50987000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr13:50985400-50987200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr13:50985600-50986400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:50985600-50986600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr13:50985600-50987200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr13:50985600-50988400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr13:50985800-50987600	Enhancers	Hela-S3	cervix
43	chr13:50985800-50987800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr13:50985800-50987800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr13:50985800-50991200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr13:50985800-50991200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr13:50985800-50991600	Weak transcription	Left Ventricle	heart
48	chr13:50986000-50986800	Enhancers	K562	blood
49	chr13:50986000-50987000	Enhancers	A549	lung
50	chr13:50986000-50991600	Weak transcription	HepG2	liver

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