Variant report

Variant	rs2526488
Chromosome Location	chr17:20098617-20098618
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20096735..20100140-chr17:20107698..20112138,4	K562	blood:
2	chr17:20096015..20099683-chr17:20108650..20110634,3	MCF-7	breast:
3	chr17:20097809..20099634-chr17:20110030..20112138,2	K562	blood:
4	chr17:20092728..20094832-chr17:20098161..20099795,2	K562	blood:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1009082	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10438824	1.00[ASN][1000 genomes]
rs11654025	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11870147	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871827	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871945	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451216	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12937827	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12941200	1.00[ASN][1000 genomes]
rs12947950	1.00[ASN][1000 genomes]
rs12948178	1.00[ASN][1000 genomes]
rs12949485	1.00[ASN][1000 genomes]
rs12952398	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1373147	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544421	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561974	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686622	1.00[ASN][1000 genomes]
rs17686798	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17686839	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17759923	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17759959	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1812934	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985810	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992562	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005722	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2013441	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013576	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034109	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058971	0.84[EUR][1000 genomes]
rs2080673	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107566	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120282	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158473	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165897	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189710	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263175	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386429	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526462	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2526464	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526467	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526468	1.00[ASN][1000 genomes]
rs2526469	1.00[ASN][1000 genomes]
rs2526470	1.00[ASN][1000 genomes]
rs2526471	1.00[ASN][1000 genomes]
rs2526472	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526473	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2526474	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526475	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526480	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526483	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526484	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526490	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526491	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2526492	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703772	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703773	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703774	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703778	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703779	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703780	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703782	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703784	1.00[ASN][1000 genomes]
rs2703785	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703787	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703789	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703790	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703791	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703792	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703794	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703797	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703799	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703801	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703802	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703804	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703806	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703808	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703810	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703811	0.81[AMR][1000 genomes]
rs2703813	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2703815	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703816	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703817	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703818	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703820	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703821	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34089239	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34644796	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712254	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35041742	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35103332	0.83[ASN][1000 genomes]
rs35429894	0.84[EUR][1000 genomes]
rs36051592	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3850782	0.84[EUR][1000 genomes]
rs3850783	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850784	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850785	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588033	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924808	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924809	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924810	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925088	0.86[AMR][1000 genomes]
rs4925089	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066869	1.00[ASN][1000 genomes]
rs62067558	1.00[ASN][1000 genomes]
rs6587063	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587064	0.83[ASN][1000 genomes]
rs7207611	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223488	0.83[ASN][1000 genomes]
rs8070401	1.00[ASN][1000 genomes]
rs8071665	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074047	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079701	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325894	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972966	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9892630	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896221	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896709	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897328	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9900166	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904928	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905493	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913818	0.82[EUR][1000 genomes]
rs9915059	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915628	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
4	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
5	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	37 gene(s)	inside rSNPs	diseases
8	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1057870	chr17:20079146-20121848	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2526488	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20093000-20099600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:20094200-20103800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr17:20094200-20105400	Weak transcription	Gastric	stomach
4	chr17:20094600-20099400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:20094600-20101000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:20094600-20105400	Weak transcription	K562	blood
7	chr17:20094800-20105600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:20095200-20101600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr17:20095400-20104800	Weak transcription	HMEC	breast
10	chr17:20095600-20099600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:20096000-20103600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr17:20096200-20100600	Enhancers	Hela-S3	cervix
13	chr17:20096200-20101000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr17:20096400-20100800	Weak transcription	Aorta	Aorta
15	chr17:20096800-20103400	Weak transcription	Brain Angular Gyrus	brain
16	chr17:20097000-20101600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr17:20097200-20099800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr17:20097200-20100200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
19	chr17:20097200-20100600	Weak transcription	Brain Anterior Caudate	brain
20	chr17:20097400-20098800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:20097600-20107800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr17:20097800-20099600	Weak transcription	Brain Substantia Nigra	brain
23	chr17:20098000-20099800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
24	chr17:20098000-20100000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
25	chr17:20098000-20102400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:20098400-20099400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr17:20098400-20100800	Weak transcription	Brain Hippocampus Middle	brain

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