Variant report

Variant	rs189332
Chromosome Location	chr11:72380252-72380253
allele	A/G
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	WRNIP1	chr11:72379301-72380486	GM12878	blood:	n/a	n/a
2	ZNF143	chr11:72379523-72380321	GM12878	blood:	n/a	chr11:72379712-72379730 chr11:72379714-72379723
3	EBF1	chr11:72379577-72380947	GM12878	blood:	n/a	n/a
4	RUNX3	chr11:72379510-72380412	GM12878	blood:	n/a	n/a
5	MTA3	chr11:72379440-72381191	GM12878	blood:	n/a	n/a
6	PML	chr11:72379614-72380300	GM12878	blood:	n/a	n/a
7	USF2	chr11:72379487-72380284	GM12878	blood:	n/a	n/a
8	PAX5	chr11:72379459-72380255	GM12878	blood:	n/a	n/a
9	FOXM1	chr11:72379610-72380510	GM12878	blood:	n/a	n/a
10	TBL1XR1	chr11:72379664-72380307	GM12878	blood:	n/a	n/a
11	CHD1	chr11:72380165-72380299	GM12878	blood:	n/a	n/a
12	NRF1	chr11:72380081-72380281	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PDE2A	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10793036	0.81[CHB][hapmap]
rs11235556	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11235557	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235558	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235559	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12146545	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12362256	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12363065	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12576046	0.86[ASN][1000 genomes]
rs12576058	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12786302	0.84[ASN][1000 genomes]
rs12787293	0.86[ASN][1000 genomes]
rs12797368	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12797791	0.93[CHB][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12799451	0.86[ASN][1000 genomes]
rs12802369	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12804316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1391888	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs163694	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs168175	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1872126	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1980089	0.81[CHB][hapmap]
rs2035467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037030	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306609	0.89[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs341051	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs341052	0.93[CHB][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs341053	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs341060	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs341061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs341062	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34142547	0.86[ASN][1000 genomes]
rs34173798	0.80[ASN][1000 genomes]
rs342322	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34285624	0.86[ASN][1000 genomes]
rs34802028	0.86[ASN][1000 genomes]
rs35748558	0.86[ASN][1000 genomes]
rs3758934	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3758935	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3758936	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3781913	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs455611	0.82[ASN][1000 genomes]
rs458275	0.94[CHB][hapmap];0.90[CHD][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs458575	0.81[CHB][hapmap]
rs56133505	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7119321	0.82[ASN][1000 genomes]
rs7126790	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs900613	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs900614	0.89[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs900615	0.85[EUR][1000 genomes]
rs90409	0.86[CHB][hapmap]
rs907853	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs907854	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs907856	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs907857	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs907858	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs932074	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs932075	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][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	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	esv1832864	chr11:72270965-72389125	Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832207	chr11:72272750-72469122	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
4	nsv523601	chr11:72281884-72430935	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
5	nsv825991	chr11:72320642-72385221	Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs189332	ARAP1	cis	cerebellum	SCAN
rs189332	KRTAP5-10	cis	parietal	SCAN
rs189332	STARD10	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72379000-72384000	Enhancers	Fetal Brain Male	brain
2	chr11:72379200-72384800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr11:72379400-72382000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr11:72379600-72380400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:72379600-72380600	Bivalent Enhancer	HSMMtube	muscle
6	chr11:72379600-72380800	Enhancers	Fetal Heart	heart
7	chr11:72379600-72381000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:72379600-72381000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:72379600-72381200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:72379800-72380400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:72379800-72380600	Weak transcription	Brain Angular Gyrus	brain
12	chr11:72380000-72380800	Enhancers	Brain Anterior Caudate	brain
13	chr11:72380000-72381000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:72380200-72380400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:72380200-72380400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
16	chr11:72380200-72380600	Enhancers	Fetal Brain Female	brain
17	chr11:72380200-72380600	Enhancers	Left Ventricle	heart
18	chr11:72380200-72380600	Enhancers	Right Ventricle	heart
19	chr11:72380200-72380600	Flanking Active TSS	GM12878-XiMat	blood
20	chr11:72380200-72381000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:72380200-72381000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:72380200-72381200	Enhancers	Brain Hippocampus Middle	brain

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