Variant report

Variant	rs12942428
Chromosome Location	chr17:46529501-46529502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46524023..46526457-chr17:46528439..46531393,2	K562	blood:
2	chr17:46523875..46525523-chr17:46528781..46531393,2	K562	blood:
3	chr17:46529355..46532196-chr17:46660157..46661823,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1027895	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1396868	0.80[ASN][1000 genomes]
rs1553750	0.80[ASN][1000 genomes]
rs1858162	0.93[ASN][1000 genomes]
rs4267363	0.92[ASN][1000 genomes]
rs4794674	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794678	0.97[ASN][1000 genomes]
rs6504256	0.93[ASN][1000 genomes]
rs7209010	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7211636	0.94[ASN][1000 genomes]
rs7211780	0.93[ASN][1000 genomes]
rs7212325	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8073326	0.89[ASN][1000 genomes]
rs9747116	0.92[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	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv2761960	chr17:46504489-46529846	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12942428	SKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46520600-46530800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:46527000-46530600	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr17:46527400-46530600	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr17:46527400-46530800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:46527600-46530800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr17:46527600-46530800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr17:46527600-46530800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr17:46527800-46530800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr17:46528000-46530200	Weak transcription	Primary B cells from cord blood	blood
10	chr17:46528200-46530600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr17:46528200-46530800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr17:46528200-46530800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:46528200-46530800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr17:46528400-46530600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:46528800-46530800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:46528800-46535200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:46529000-46535400	Enhancers	Fetal Thymus	thymus
18	chr17:46529200-46530000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr17:46529200-46530800	Weak transcription	K562	blood
20	chr17:46529200-46532400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr17:46529200-46533800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr17:46529400-46530400	Enhancers	Primary T cells from cord blood	blood
23	chr17:46529400-46530400	Weak transcription	GM12878-XiMat	blood

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