Variant report

Variant	rs11884072
Chromosome Location	chr2:180403128-180403129
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	GATA3	chr2:180403093-180403731	SK-N-SH	brain:	n/a	chr2:180403660-180403667
2	TCF12	chr2:180403046-180403736	SK-N-SH	brain:	n/a	n/a
3	FOS	chr2:180403013-180403672	MCF10A-Er-Src	breast:	n/a	chr2:180403277-180403289 chr2:180403279-180403287
4	TCF12	chr2:180402973-180403728	SK-N-SH	brain:	n/a	n/a
5	EP300	chr2:180403015-180403714	SK-N-SH	brain:	n/a	n/a
6	FOSL2	chr2:180403027-180403672	SK-N-SH	brain:	n/a	chr2:180403277-180403289 chr2:180403279-180403287
7	NFIC	chr2:180403033-180403601	SK-N-SH	brain:	n/a	n/a
8	JUND	chr2:180403023-180403686	SK-N-SH	brain:	n/a	chr2:180403277-180403289 chr2:180403279-180403287
9	TEAD4	chr2:180403073-180403670	SK-N-SH	brain:	n/a	n/a
10	FOS	chr2:180403109-180403540	MCF10A-Er-Src	breast:	n/a	chr2:180403277-180403289 chr2:180403279-180403287
11	STAT3	chr2:180403107-180403425	MCF10A-Er-Src	breast:	n/a	n/a
12	NFIC	chr2:180403066-180403537	SK-N-SH	brain:	n/a	n/a
13	STAT3	chr2:180403073-180403386	MCF10A-Er-Src	breast:	n/a	n/a
14	GATA3	chr2:180402960-180403724	SK-N-SH	brain:	n/a	chr2:180403660-180403667
15	MEF2A	chr2:180402999-180403580	SK-N-SH	brain:	n/a	chr2:180403279-180403287 chr2:180403035-180403050
16	FOS	chr2:180403105-180403533	MCF10A-Er-Src	breast:	n/a	chr2:180403277-180403289 chr2:180403279-180403287
17	FOSL2	chr2:180403087-180403528	SK-N-SH	brain:	n/a	chr2:180403277-180403289 chr2:180403279-180403287
18	FOS	chr2:180403103-180403536	MCF10A-Er-Src	breast:	n/a	chr2:180403277-180403289 chr2:180403279-180403287
19	PBX3	chr2:180403086-180403645	SK-N-SH	brain:	n/a	n/a
20	STAT3	chr2:180403122-180403385	MCF10A-Er-Src	breast:	n/a	n/a
21	PBX3	chr2:180403088-180403687	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ZNF385B	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12693194	1.00[CHD][hapmap]
rs1515295	0.81[MEX][hapmap]
rs1515297	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs16866767	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17816284	1.00[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6433796	1.00[CHD][hapmap];0.81[MEX][hapmap];0.82[YRI][hapmap]
rs6709838	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73976407	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875470	chr2:180400021-180432529	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv523865	chr2:180403128-180426764	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11884072	PDE1A	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180397800-180403600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:180401600-180403400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:180401800-180403400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:180402400-180403800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:180402600-180403800	Enhancers	Osteobl	bone
6	chr2:180402800-180403200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:180402800-180403600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:180402800-180403600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:180402800-180403600	Strong transcription	Liver	Liver
10	chr2:180402800-180403800	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links