Variant report

Variant	rs40211
Chromosome Location	chr5:53180890-53180891
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	EP300	chr5:53180821-53181054	K562	blood:	n/a	n/a
2	CEBPB	chr5:53180586-53181080	IMR90	lung:	n/a	chr5:53180940-53180951
3	JUND	chr5:53180795-53181113	K562	blood:	n/a	n/a
4	CEBPB	chr5:53180853-53181114	K562	blood:	n/a	chr5:53180940-53180951
5	CEBPB	chr5:53180837-53181056	HepG2	liver:	n/a	chr5:53180940-53180951
6	CEBPB	chr5:53180664-53181106	Hela-S3	cervix:	n/a	chr5:53180940-53180951

Variant related genes	Relation type
ENSG00000272416	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1027210	0.88[GIH][hapmap]
rs175248	1.00[EUR][1000 genomes]
rs1979646	1.00[EUR][1000 genomes]
rs1979647	1.00[EUR][1000 genomes]
rs1981842	1.00[EUR][1000 genomes]
rs199609	0.94[ASN][1000 genomes]
rs2042313	0.85[GIH][hapmap];1.00[EUR][1000 genomes]
rs271207	1.00[EUR][1000 genomes]
rs271208	0.94[GIH][hapmap];1.00[EUR][1000 genomes]
rs271243	0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs271245	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs271250	0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs271257	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs271259	0.85[ASN][1000 genomes]
rs271261	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs37539	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs37540	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776740	1.00[EUR][1000 genomes]
rs3797287	1.00[EUR][1000 genomes]
rs3797290	1.00[EUR][1000 genomes]
rs40212	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450173	1.00[EUR][1000 genomes]
rs7733347	0.88[GIH][hapmap];1.00[EUR][1000 genomes]

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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv830298	chr5:52973912-53193398	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv533778	chr5:53092696-53284566	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53170200-53181800	Weak transcription	Spleen	Spleen
2	chr5:53173800-53227800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:53174200-53186400	Weak transcription	Left Ventricle	heart
4	chr5:53174400-53211000	Weak transcription	K562	blood
5	chr5:53175400-53183400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:53175400-53186400	Weak transcription	Primary T cells from cord blood	blood
7	chr5:53176000-53187200	Weak transcription	Esophagus	oesophagus
8	chr5:53176600-53189000	Weak transcription	Fetal Intestine Large	intestine
9	chr5:53176600-53190400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:53176800-53181000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:53177000-53212800	Weak transcription	Fetal Intestine Small	intestine
12	chr5:53177400-53181000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr5:53177400-53188600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:53177600-53182400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:53177600-53189000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr5:53178000-53181000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:53178000-53190800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:53178400-53190800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:53178800-53186600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:53179200-53181400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr5:53179200-53183200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr5:53179200-53186400	Weak transcription	NHLF	lung
23	chr5:53179200-53187200	Weak transcription	Lung	lung
24	chr5:53179400-53182600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr5:53179800-53182200	Enhancers	Dnd41	blood
26	chr5:53180000-53187400	Weak transcription	Fetal Stomach	stomach
27	chr5:53180000-53194200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:53180200-53181000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:53180200-53181200	Enhancers	NHDF-Ad	bronchial
30	chr5:53180400-53181000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr5:53180400-53181000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:53180400-53181000	Enhancers	HSMMtube	muscle
33	chr5:53180400-53181200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:53180400-53182000	Weak transcription	Gastric	stomach
35	chr5:53180600-53181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:53180600-53186400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:53180800-53181800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:53180800-53182000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:53180800-53182000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:53180800-53187000	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links