Variant report

Variant	rs1396354
Chromosome Location	chr8:118632412-118632413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:118619974..118622515-chr8:118630290..118632485,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10089009	0.93[EUR][1000 genomes]
rs10093232	0.89[EUR][1000 genomes]
rs10093382	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10100465	0.83[EUR][1000 genomes]
rs10108248	0.89[EUR][1000 genomes]
rs10955822	0.89[EUR][1000 genomes]
rs10955823	0.83[EUR][1000 genomes]
rs1160474	0.93[EUR][1000 genomes]
rs13254406	0.91[EUR][1000 genomes]
rs13280410	0.90[EUR][1000 genomes]
rs13439042	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1383176	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1396351	0.83[EUR][1000 genomes]
rs1508555	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1508569	0.86[EUR][1000 genomes]
rs16890041	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17753197	0.88[EUR][1000 genomes]
rs218017	0.83[CEU][hapmap]
rs218018	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs2202792	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2202793	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2202794	0.91[EUR][1000 genomes]
rs34660998	0.88[EUR][1000 genomes]
rs4604472	0.89[EUR][1000 genomes]
rs4876727	0.95[EUR][1000 genomes]
rs6469700	0.81[EUR][1000 genomes]
rs7815693	0.83[EUR][1000 genomes]
rs7838659	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019636	chr8:118598433-118946091	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv539734	chr8:118598433-118946091	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1028387	chr8:118602105-118640162	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1396354	PAPPA	trans	cerebellum	SCAN
rs1396354	NT5M	trans	parietal	SCAN
rs1396354	ENPP2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118627600-118636400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:118629000-118636200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr8:118630000-118632600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:118630400-118633200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:118630400-118633600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr8:118630600-118632800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:118630600-118632800	Enhancers	HSMM	muscle
8	chr8:118630600-118633400	Enhancers	NHEK	skin
9	chr8:118630600-118633800	Enhancers	HMEC	breast
10	chr8:118630600-118634600	Enhancers	NHDF-Ad	bronchial
11	chr8:118630800-118633800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr8:118630800-118634800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr8:118630800-118635400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:118631000-118633000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr8:118631000-118633200	Enhancers	Hela-S3	cervix
16	chr8:118631000-118635600	Enhancers	NH-A	brain
17	chr8:118631000-118635600	Enhancers	Osteobl	bone
18	chr8:118631200-118632800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr8:118631200-118633200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr8:118631400-118632600	Enhancers	HSMMtube	muscle
21	chr8:118631400-118632800	Enhancers	NHLF	lung
22	chr8:118631800-118632600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:118632000-118632600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr8:118632000-118632600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr8:118632200-118632600	Enhancers	Aorta	Aorta
26	chr8:118632400-118635200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr8:118632400-118636600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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