Variant report

Variant	rs1320163
Chromosome Location	chr3:43303296-43303297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43294226..43299346-chr3:43301138..43304009,5	K562	blood:
2	chr3:43296454..43299346-chr3:43300698..43303972,3	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10514709	0.97[ASN][1000 genomes]
rs12486205	0.85[ASN][1000 genomes]
rs1317402	0.99[EUR][1000 genomes]
rs1320160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075328	0.93[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17075375	0.82[ASN][1000 genomes]
rs17075379	0.82[ASN][1000 genomes]
rs17075391	0.82[ASN][1000 genomes]
rs17075395	0.85[ASN][1000 genomes]
rs17075409	1.00[ASN][1000 genomes]
rs17075415	0.99[EUR][1000 genomes]
rs17254504	0.98[EUR][1000 genomes]
rs17254786	0.98[EUR][1000 genomes]
rs17320570	0.98[EUR][1000 genomes]
rs17405916	0.87[EUR][1000 genomes]
rs1878721	0.82[ASN][1000 genomes]
rs1996497	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2372350	0.98[EUR][1000 genomes]
rs2372351	0.98[EUR][1000 genomes]
rs2372360	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2372361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4504148	0.98[EUR][1000 genomes]
rs4580522	0.97[ASN][1000 genomes]
rs4682883	1.00[JPT][hapmap]
rs55650554	0.98[EUR][1000 genomes]
rs55836177	0.84[EUR][1000 genomes]
rs55919553	0.98[EUR][1000 genomes]
rs55988644	0.98[EUR][1000 genomes]
rs55990908	0.98[EUR][1000 genomes]
rs56032317	0.96[EUR][1000 genomes]
rs56053383	0.96[EUR][1000 genomes]
rs56291522	0.98[EUR][1000 genomes]
rs56412846	0.99[EUR][1000 genomes]
rs56745072	0.98[EUR][1000 genomes]
rs57757985	0.98[EUR][1000 genomes]
rs58504881	0.96[EUR][1000 genomes]
rs60971695	0.98[EUR][1000 genomes]
rs6766079	0.98[EUR][1000 genomes]
rs6767019	0.99[EUR][1000 genomes]
rs6791341	0.98[EUR][1000 genomes]
rs6791526	0.93[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6796424	0.93[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6798292	0.93[ASN][1000 genomes]
rs6800990	0.85[ASN][1000 genomes]
rs6801151	0.94[EUR][1000 genomes]
rs6805108	0.98[EUR][1000 genomes]
rs6808396	0.95[EUR][1000 genomes]
rs73072908	0.98[EUR][1000 genomes]
rs73072912	0.97[EUR][1000 genomes]
rs73072920	0.98[EUR][1000 genomes]
rs73086702	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73088703	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73088726	0.97[EUR][1000 genomes]
rs73088732	0.98[EUR][1000 genomes]
rs73088738	0.98[EUR][1000 genomes]
rs73088748	0.97[EUR][1000 genomes]
rs73088757	0.98[EUR][1000 genomes]
rs73829200	0.98[EUR][1000 genomes]
rs7633546	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7634209	0.93[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7641590	0.97[EUR][1000 genomes]
rs7646966	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1320163	SLC25A38	cis	parietal	SCAN
rs1320163	SNRK	cis	cerebellum	SCAN
rs1320163	PTH1R	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43296800-43305800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:43299400-43303400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:43299800-43306400	Weak transcription	Spleen	Spleen
4	chr3:43299800-43308200	Weak transcription	Right Atrium	heart
5	chr3:43300400-43305800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:43300400-43305800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:43300600-43305800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:43300600-43306000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:43302000-43303800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:43302000-43314000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:43302200-43304000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:43302400-43310000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:43303200-43304200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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