Variant report

Variant	rs12550896
Chromosome Location	chr9:2255632-2255633
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2255030..2255773-chr9:2600478..2601011,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10738622	0.92[JPT][hapmap]
rs10738636	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10757326	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10757347	0.84[EUR][1000 genomes]
rs10757349	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811693	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10811709	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10811710	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10811711	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10811724	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10811727	0.87[EUR][1000 genomes]
rs10811738	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811740	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811741	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811742	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811747	0.84[EUR][1000 genomes]
rs10811749	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811750	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10965348	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10965349	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10965354	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10965382	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10965383	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10965385	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10965386	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10965390	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10965392	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12376725	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12554618	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12684055	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1359259	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1408333	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1408334	0.83[JPT][hapmap]
rs16938167	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2147264	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4740667	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4741658	0.92[JPT][hapmap];0.82[MEX][hapmap]
rs7020176	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7031590	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7041362	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7847256	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7853529	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7872273	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs942399	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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 target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1033628	chr9:2215179-2303623	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv539927	chr9:2215179-2303623	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv892060	chr9:2218129-2261944	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv6457	chr9:2228493-2271756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv892061	chr9:2229694-2262889	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv1029947	chr9:2233969-2364269	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1015332	chr9:2235123-2361722	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1022726	chr9:2235500-2361890	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv539928	chr9:2235500-2361890	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv1033537	chr9:2235700-2361750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv539929	chr9:2235700-2361750	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv613127	chr9:2237390-2363874	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1018079	chr9:2248103-2271488	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv869882	chr9:2249223-2357827	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv613128	chr9:2253678-2419538	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1016677	chr9:2253741-2415423	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv1016401	chr9:2255397-2410590	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12550896	PPAPDC2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2248600-2263800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:2248800-2257000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:2252200-2260400	Weak transcription	A549	lung
4	chr9:2253600-2255800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:2254400-2255800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:2254600-2257400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:2254600-2262800	Weak transcription	Ovary	ovary
8	chr9:2255400-2260400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr9:2255400-2262800	Weak transcription	Fetal Muscle Leg	muscle
10	chr9:2255600-2255800	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr9:2255600-2257200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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