Variant report

Variant	rs2108979
Chromosome Location	chr17:19928566-19928567
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	chr17:19927266..19929867-chr17:19933852..19935376,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10083856	0.81[AMR][1000 genomes]
rs1034904	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204421	0.81[ASN][1000 genomes]
rs11871651	0.81[AMR][1000 genomes]
rs16960644	0.89[ASN][1000 genomes]
rs1860302	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2108980	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28807825	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34291370	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36034566	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3862152	0.83[AMR][1000 genomes]
rs3888318	0.83[AMR][1000 genomes]
rs3909258	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4005937	0.83[AMR][1000 genomes]
rs4479308	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4479309	0.80[AMR][1000 genomes]
rs4570919	0.80[AMR][1000 genomes]
rs4924801	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924806	0.80[AMR][1000 genomes]
rs4925065	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925066	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925067	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925069	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4925072	0.83[AMR][1000 genomes]
rs4925073	0.82[AMR][1000 genomes]
rs56142708	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62067555	0.80[AMR][1000 genomes]
rs7207625	0.80[AMR][1000 genomes]
rs7208025	0.80[AMR][1000 genomes]
rs7208365	0.80[AMR][1000 genomes]
rs7208635	0.80[AMR][1000 genomes]
rs7209734	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7211535	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7215514	0.82[ASN][1000 genomes]
rs7218708	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7223305	0.80[AMR][1000 genomes]
rs8065337	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8067545	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs888423	0.80[AMR][1000 genomes]
rs918228	0.80[AMR][1000 genomes]
rs9889743	0.81[AMR][1000 genomes]
rs9891739	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9897246	0.83[AMR][1000 genomes]
rs9906625	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9907788	0.82[AMR][1000 genomes]
rs9909009	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9915758	0.83[AMR][1000 genomes]
rs9916675	0.82[ASN][1000 genomes]
rs9944451	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2108979	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19914600-19938400	Weak transcription	Brain Hippocampus Middle	brain
2	chr17:19921600-19931600	Weak transcription	Ovary	ovary
3	chr17:19922200-19935800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:19923400-19930800	Weak transcription	K562	blood
5	chr17:19923400-19956600	Weak transcription	A549	lung
6	chr17:19923600-19946400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:19926200-19932400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr17:19926400-19947000	Weak transcription	Brain Angular Gyrus	brain
9	chr17:19926800-19930200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:19928400-19928600	Enhancers	Aorta	Aorta
11	chr17:19928400-19937000	Weak transcription	Brain Cingulate Gyrus	brain

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