Variant report

Variant	rs2108980
Chromosome Location	chr17:19920518-19920519
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	chr17:19920482..19924140-chr17:19925056..19928088,3	K562	blood:
2	chr17:19920482..19923418-chr17:19925056..19926858,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10083856	0.84[AMR][1000 genomes]
rs1034904	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204420	0.81[AFR][1000 genomes]
rs11204421	0.84[ASN][1000 genomes]
rs11867585	0.82[AMR][1000 genomes]
rs11871651	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16960644	0.84[ASN][1000 genomes]
rs1860302	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108979	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28603224	0.82[AMR][1000 genomes]
rs28637614	0.82[AMR][1000 genomes]
rs28666381	0.82[AMR][1000 genomes]
rs28807825	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34290687	0.81[AMR][1000 genomes]
rs34291370	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34401389	0.81[AMR][1000 genomes]
rs35003563	0.81[AMR][1000 genomes]
rs36034566	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36077949	0.82[AMR][1000 genomes]
rs3862152	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3888318	0.86[AMR][1000 genomes]
rs3909258	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4005937	0.86[AMR][1000 genomes]
rs4267380	0.81[AMR][1000 genomes]
rs4479308	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4479309	0.83[AMR][1000 genomes]
rs4570919	0.83[AMR][1000 genomes]
rs4924801	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924803	0.81[AMR][1000 genomes]
rs4924806	0.83[AMR][1000 genomes]
rs4925065	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925066	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925069	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4925072	0.86[AMR][1000 genomes]
rs4925073	0.85[AMR][1000 genomes]
rs4925077	0.81[AMR][1000 genomes]
rs4925079	0.82[AMR][1000 genomes]
rs4925081	0.81[AMR][1000 genomes]
rs4925085	0.80[AMR][1000 genomes]
rs56142708	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62067555	0.83[AMR][1000 genomes]
rs6587206	0.80[AFR][1000 genomes]
rs7207625	0.83[AMR][1000 genomes]
rs7208025	0.83[AMR][1000 genomes]
rs7208365	0.83[AMR][1000 genomes]
rs7208635	0.83[AMR][1000 genomes]
rs7209734	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7211535	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7215514	0.83[ASN][1000 genomes]
rs7218708	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7223305	0.83[AMR][1000 genomes]
rs8065337	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8067545	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs888423	0.83[AMR][1000 genomes]
rs918228	0.83[AMR][1000 genomes]
rs9889743	0.84[AMR][1000 genomes]
rs9891739	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9896411	0.82[AMR][1000 genomes]
rs9897246	0.86[AMR][1000 genomes]
rs9897653	0.81[AMR][1000 genomes]
rs9906625	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9907788	0.85[AMR][1000 genomes]
rs9909009	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9912775	0.81[AMR][1000 genomes]
rs9915758	0.86[AMR][1000 genomes]
rs9916675	0.85[ASN][1000 genomes]
rs9944451	0.83[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	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2108980	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19913800-19921200	Weak transcription	Aorta	Aorta
2	chr17:19914200-19925000	Weak transcription	Adipose Nuclei	Adipose
3	chr17:19914600-19920600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:19914600-19920800	Weak transcription	Brain Anterior Caudate	brain
5	chr17:19914600-19922000	Weak transcription	Brain Angular Gyrus	brain
6	chr17:19914600-19928000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr17:19914600-19938400	Weak transcription	Brain Hippocampus Middle	brain
8	chr17:19918000-19922000	Weak transcription	K562	blood
9	chr17:19918800-19921200	Weak transcription	Ovary	ovary
10	chr17:19920000-19923600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr17:19920200-19923400	Strong transcription	A549	lung
12	chr17:19920400-19922200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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