Variant report

Variant	rs2032500
Chromosome Location	chr6:28854269-28854270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28852918..28854862-chr6:28890133..28892224,2	K562	blood:
2	chr6:28847771..28851189-chr6:28852484..28857224,5	MCF-7	breast:
3	chr6:28853392..28856962-chr6:28946124..28948045,3	K562	blood:

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1002925	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1005123	0.81[ASN][1000 genomes]
rs1233602	0.83[EUR][1000 genomes]
rs1237485	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1476016	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs169683	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1794587	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs184093	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2013848	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2071785	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2071790	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209122	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209126	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209128	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs209129	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs209137	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209138	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209148	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs209149	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs209152	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209153	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209160	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs209161	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs209163	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs209164	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209169	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs209171	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs209173	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209175	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs209176	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209179	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209182	0.86[EUR][1000 genomes]
rs209184	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209186	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2157312	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2157313	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2187807	0.88[ASN][1000 genomes]
rs2187808	0.88[ASN][1000 genomes]
rs2208536	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2269555	0.82[ASN][1000 genomes]
rs2754764	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2754767	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2765218	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2765219	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2765229	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129792	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129793	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130841	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130842	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130886	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130889	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130897	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131070	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131074	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131077	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131100	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3131102	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3131342	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3132371	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3132386	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3135303	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3135315	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135319	0.80[EUR][1000 genomes]
rs3135321	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3135322	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3135323	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3135324	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3135326	0.84[EUR][1000 genomes]
rs3135327	0.87[EUR][1000 genomes]
rs3135328	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs377392	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs381808	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs386628	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs393431	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4427026	0.86[ASN][1000 genomes]
rs4713186	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4713187	0.86[ASN][1000 genomes]
rs4713188	0.87[ASN][1000 genomes]
rs4713190	0.84[ASN][1000 genomes]
rs4713192	0.84[ASN][1000 genomes]
rs4947339	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs526983	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6456857	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6456876	0.88[ASN][1000 genomes]
rs6456880	0.83[ASN][1000 genomes]
rs6456883	0.82[ASN][1000 genomes]
rs6901599	0.88[ASN][1000 genomes]
rs6904975	0.82[ASN][1000 genomes]
rs6906909	0.82[ASN][1000 genomes]
rs6914955	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6916161	0.82[ASN][1000 genomes]
rs6920392	0.84[ASN][1000 genomes]
rs6931823	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs763009	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7743189	0.85[ASN][1000 genomes]
rs7755875	0.90[ASN][1000 genomes]
rs7761547	0.86[ASN][1000 genomes]
rs9257229	0.81[EUR][1000 genomes]
rs9257401	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9257404	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9257405	0.87[ASN][1000 genomes]
rs9257421	0.87[ASN][1000 genomes]
rs9257447	0.83[ASN][1000 genomes]
rs9257449	0.83[ASN][1000 genomes]
rs9257455	0.80[ASN][1000 genomes]
rs9257461	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2032500	ZNF323	cis	parietal	SCAN
rs2032500	NKAPL	cis	parietal	SCAN
rs2032500	ZSCAN23	cis	parietal	SCAN
rs2032500	ZKSCAN3	cis	cerebellum	SCAN
rs2032500	ZNF323	cis	cerebellum	SCAN
rs2032500	HIST1H2BH	cis	cerebellum	SCAN
rs2032500	ZSCAN16	cis	parietal	SCAN
rs2032500	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28849400-28863000	Weak transcription	Right Atrium	heart
2	chr6:28853400-28863000	Weak transcription	Fetal Kidney	kidney
3	chr6:28853800-28854400	ZNF genes & repeats	K562	blood
4	chr6:28854000-28854400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:28854200-28854400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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