Variant report

Variant	rs2952289
Chromosome Location	chr17:66464414-66464415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:66458968..66465648-chr17:66506510..66510180,10	MCF-7	breast:
2	chr17:66460499..66464491-chr17:66506500..66510531,5	MCF-7	breast:
3	chr17:66459308..66461889-chr17:66462514..66465217,2	K562	blood:
4	chr17:66463233..66464971-chr17:66754716..66757139,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11868680	0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1808335	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2111508	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302783	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2909207	0.81[GIH][hapmap]
rs2909209	0.88[ASN][1000 genomes]
rs2909211	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2909213	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2909216	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909218	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909220	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2909221	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2952279	0.83[CHB][hapmap];0.81[GIH][hapmap]
rs2952280	0.83[CHB][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs2952283	0.82[EUR][1000 genomes]
rs2952286	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2952290	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952294	0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs2952295	0.88[ASN][1000 genomes]
rs2952296	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs71378928	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883541	0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2952289	PITPNC1	cis	cerebellum	SCAN
rs2952289	PRKAR1A	cis	Artery Tibial	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66454600-66465200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:66454600-66470400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:66456800-66470400	Weak transcription	Right Ventricle	heart
4	chr17:66459200-66466200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:66460400-66470400	Weak transcription	Ovary	ovary
6	chr17:66461400-66465200	Enhancers	Fetal Muscle Leg	muscle
7	chr17:66462600-66467600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:66462800-66470400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr17:66463400-66465800	Flanking Active TSS	Fetal Heart	heart
10	chr17:66463600-66465200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr17:66464000-66465200	Enhancers	Aorta	Aorta
12	chr17:66464000-66465800	Enhancers	HSMM	muscle
13	chr17:66464200-66464800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:66464200-66464800	Enhancers	NHLF	lung
15	chr17:66464200-66465200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr17:66464200-66465200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr17:66464200-66465600	Enhancers	NH-A	brain
18	chr17:66464200-66468600	Weak transcription	Left Ventricle	heart
19	chr17:66464400-66464600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr17:66464400-66464600	Flanking Active TSS	HSMMtube	muscle
21	chr17:66464400-66464600	Enhancers	Osteobl	bone
22	chr17:66464400-66465200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr17:66464400-66465200	Enhancers	NHDF-Ad	bronchial
24	chr17:66464400-66465400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:66464400-66465800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:66464400-66465800	Enhancers	HepG2	liver

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