Variant report

Variant	rs56142708
Chromosome Location	chr17:19934963-19934964
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19927266..19929867-chr17:19933852..19935376,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1034904	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10459969	0.85[ASN][1000 genomes]
rs10459970	0.85[ASN][1000 genomes]
rs1860302	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2108979	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2108980	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2385960	0.85[ASN][1000 genomes]
rs28807825	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34291370	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36034566	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3909258	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924801	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925065	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4925066	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925067	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925069	0.86[AMR][1000 genomes]
rs57040439	0.85[ASN][1000 genomes]
rs57673732	0.85[ASN][1000 genomes]
rs58313980	0.85[ASN][1000 genomes]
rs7209734	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7211535	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7218708	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843506	0.85[ASN][1000 genomes]
rs73984559	0.85[ASN][1000 genomes]
rs8065337	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8067545	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8073875	0.85[ASN][1000 genomes]
rs9889743	0.81[AMR][1000 genomes]
rs9891739	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9912775	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56142708	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19914600-19938400	Weak transcription	Brain Hippocampus Middle	brain
2	chr17:19922200-19935800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:19923400-19956600	Weak transcription	A549	lung
4	chr17:19923600-19946400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr17:19926400-19947000	Weak transcription	Brain Angular Gyrus	brain
6	chr17:19928400-19937000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr17:19932000-19956800	Weak transcription	Ovary	ovary
8	chr17:19932400-19935200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr17:19932600-19936000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr17:19934000-19935000	Enhancers	GM12878-XiMat	blood

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