Variant report

Variant	rs942399
Chromosome Location	chr9:2261944-2261945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10738622	0.92[JPT][hapmap]
rs10738636	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10757326	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10757347	0.87[EUR][1000 genomes]
rs10757349	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10811693	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811709	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10811710	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10811711	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10811724	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10811727	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10811738	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10811740	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10811741	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10811742	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10811747	0.87[EUR][1000 genomes]
rs10811749	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10811750	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10965323	0.82[MEX][hapmap]
rs10965348	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10965349	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10965354	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10965382	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10965383	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10965385	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10965386	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10965390	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10965392	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12376725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12550896	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12554618	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12684055	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1359259	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1408333	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1408334	0.83[JPT][hapmap]
rs16938167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2147264	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4740667	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4741658	0.92[JPT][hapmap];0.87[MEX][hapmap]
rs7020176	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7031590	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7040506	0.80[AMR][1000 genomes]
rs7041362	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7847256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853529	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7860216	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7872273	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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
24	nsv613129	chr9:2256092-2330907	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv466079	chr9:2261944-2274492	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
26	nsv613130	chr9:2261944-2274492	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs942399	PPAPDC2	cis	cerebellum	SCAN

Chromatin state (count:31 , 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	chr9:2254600-2262800	Weak transcription	Ovary	ovary
3	chr9:2255400-2262800	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:2256200-2263200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:2257400-2275000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:2257600-2262800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:2258000-2263000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:2258200-2263000	Weak transcription	Primary B cells from cord blood	blood
9	chr9:2258400-2266200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:2260400-2262000	Enhancers	A549	lung
11	chr9:2260400-2263600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:2260800-2262400	Weak transcription	Fetal Brain Male	brain
13	chr9:2261000-2262000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:2261000-2262200	Weak transcription	Brain Substantia Nigra	brain
15	chr9:2261000-2262800	Weak transcription	Fetal Brain Female	brain
16	chr9:2261000-2268000	Weak transcription	Left Ventricle	heart
17	chr9:2261200-2262400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:2261200-2262400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:2261200-2262600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:2261200-2262800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr9:2261200-2267200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:2261400-2262200	Weak transcription	Brain Germinal Matrix	brain
23	chr9:2261400-2263000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:2261400-2267800	Weak transcription	Psoas Muscle	Psoas
25	chr9:2261600-2262600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:2261600-2262600	Weak transcription	Osteobl	bone
27	chr9:2261600-2262800	Weak transcription	NH-A	brain
28	chr9:2261800-2262200	Weak transcription	Fetal Lung	lung
29	chr9:2261800-2263000	Weak transcription	Right Atrium	heart
30	chr9:2261800-2267000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr9:2261800-2267200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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