Variant report

Variant	rs538218
Chromosome Location	chr15:43479328-43479329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:43479151-43479350	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr15:43479200-43479350	AG09319	gingival:	n/a	n/a
3	MXI1	chr15:43476643-43479389	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr15:43479253-43479429	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:43478456..43479959-chr15:43502893..43504984,2	K562	blood:
2	chr15:43476285..43479868-chr15:43558571..43560739,3	K562	blood:
3	chr15:43478839..43481750-chr15:43486043..43488157,2	K562	blood:
4	chr15:43414543..43416437-chr15:43476770..43479731,2	K562	blood:
5	chr15:43477582..43480144-chr15:43497635..43499944,2	K562	blood:
6	chr15:43413837..43416869-chr15:43476770..43480897,4	K562	blood:
7	chr15:43471322..43474436-chr15:43477554..43479456,3	K562	blood:
8	chr15:43212538..43214244-chr15:43477789..43479955,2	K562	blood:
9	chr15:43479061..43481710-chr15:43621878..43623729,2	K562	blood:
10	chr15:43478113..43480240-chr15:43513375..43516202,2	K562	blood:
11	chr15:43368519..43371458-chr15:43478469..43480102,2	K562	blood:
12	chr15:43477046..43479733-chr15:43513135..43515650,2	MCF-7	breast:

No data

Variant related genes	Relation type
CCNDBP1	TF binding region
ENSG00000261687	TF binding region
ENSG00000137842	Chromatin interaction
ENSG00000261679	Chromatin interaction
ENSG00000168803	Chromatin interaction
ENSG00000166947	Chromatin interaction
ENSG00000166946	Chromatin interaction
ENSG00000168806	Chromatin interaction
ENSG00000128881	Chromatin interaction
ENSG00000104055	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11070386	0.89[CEU][hapmap];0.94[CHB][hapmap]
rs11070391	0.89[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs11070396	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070397	0.80[EUR][1000 genomes]
rs11070398	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11630595	0.89[CEU][hapmap];0.94[CHB][hapmap]
rs11855754	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12592725	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12899266	0.89[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes]
rs1462856	0.89[CEU][hapmap]
rs16957511	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1834643	0.92[EUR][1000 genomes]
rs2042742	0.94[EUR][1000 genomes]
rs2176870	0.89[LWK][hapmap]
rs2241516	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412752	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs28585036	0.86[CEU][hapmap]
rs28756768	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2899077	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2947019	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34646108	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3736054	0.83[CHB][hapmap]
rs3784267	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3784268	0.91[EUR][1000 genomes]
rs4573908	0.89[CEU][hapmap];0.94[CHB][hapmap]
rs4923955	0.89[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap]
rs4924704	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs494863	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs495286	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs497138	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs499280	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs530305	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs531850	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs540587	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493076	0.89[CEU][hapmap]
rs6493077	0.89[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap]
rs7174915	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs7183814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027371	0.83[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap]
rs8027733	0.89[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap]
rs8042481	0.89[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv1793290	chr15:43479328-43487742	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs538218	CCNDBP1	cis	lymphoblastoid	seeQTL
rs538218	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs538218	TGM5	cis	lymphoblastoid	seeQTL
rs538218	ADAL	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43477200-43479600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr15:43478200-43479400	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr15:43478600-43479400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:43478600-43480600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr15:43478600-43481400	Weak transcription	Ovary	ovary
6	chr15:43478600-43481600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:43478600-43481600	Weak transcription	Esophagus	oesophagus
8	chr15:43478600-43481600	Weak transcription	Fetal Lung	lung
9	chr15:43478600-43481600	Weak transcription	Gastric	stomach
10	chr15:43478600-43481600	Weak transcription	Lung	lung
11	chr15:43478600-43481600	Weak transcription	Spleen	Spleen
12	chr15:43478600-43482200	Weak transcription	Pancreas	Pancrea
13	chr15:43478600-43489000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:43478600-43489600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:43478600-43496200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:43478800-43479400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:43478800-43479400	Enhancers	Adipose Nuclei	Adipose
18	chr15:43478800-43479400	Enhancers	Liver	Liver
19	chr15:43478800-43479400	Enhancers	Brain Substantia Nigra	brain
20	chr15:43478800-43479400	Enhancers	Colon Smooth Muscle	Colon
21	chr15:43478800-43479400	Genic enhancers	Rectal Smooth Muscle	rectum
22	chr15:43478800-43479600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr15:43478800-43479600	Flanking Active TSS	GM12878-XiMat	blood
24	chr15:43478800-43479800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr15:43478800-43479800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:43478800-43479800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:43478800-43479800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:43478800-43480000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:43478800-43480200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr15:43478800-43480400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr15:43478800-43480400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:43478800-43480400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:43478800-43480400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr15:43478800-43480400	Weak transcription	Small Intestine	intestine
35	chr15:43478800-43480400	Weak transcription	A549	lung
36	chr15:43478800-43480600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:43478800-43480800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:43478800-43480800	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr15:43478800-43480800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:43478800-43481200	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:43478800-43481200	Weak transcription	Thymus	Thymus
42	chr15:43478800-43481400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:43478800-43481400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:43478800-43481400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:43478800-43481400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:43478800-43481400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr15:43478800-43481400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:43478800-43481400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:43478800-43481400	Weak transcription	Fetal Thymus	thymus
50	chr15:43478800-43481400	Weak transcription	HSMM	muscle

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