Variant report

Variant	rs1002925
Chromosome Location	chr6:28801383-28801384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28800000..28803653-chr6:28805218..28808820,5	K562	blood:
2	chr6:28795106..28798170-chr6:28801173..28804341,4	K562	blood:
3	chr6:28796077..28799032-chr6:28801173..28802819,3	K562	blood:

Variant related genes	Relation type
ENSG00000225173	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1233596	0.81[EUR][1000 genomes]
rs1233601	0.81[EUR][1000 genomes]
rs1233602	0.87[EUR][1000 genomes]
rs1233607	0.80[EUR][1000 genomes]
rs1233615	0.81[EUR][1000 genomes]
rs1233616	0.81[EUR][1000 genomes]
rs1233617	0.80[EUR][1000 genomes]
rs1235176	0.81[EUR][1000 genomes]
rs1237485	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1476016	0.89[EUR][1000 genomes]
rs169683	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1794587	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs184093	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2032500	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071785	0.81[ASN][1000 genomes]
rs2071790	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs209122	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209126	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209128	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209129	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209137	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209138	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs209148	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209149	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209152	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs209153	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209160	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs209161	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs209163	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs209164	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209169	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209171	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209173	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs209175	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209176	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209179	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs209182	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs209184	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs209186	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2157312	0.86[EUR][1000 genomes]
rs2157313	0.88[EUR][1000 genomes]
rs2208536	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2754764	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2754767	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2765218	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2765219	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2765229	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129792	0.83[EUR][1000 genomes]
rs3129793	0.81[EUR][1000 genomes]
rs3130841	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130842	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3130886	0.84[EUR][1000 genomes]
rs3130889	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130897	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3131070	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3131074	0.89[EUR][1000 genomes]
rs3131077	0.88[EUR][1000 genomes]
rs3131100	0.81[EUR][1000 genomes]
rs3131102	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131342	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3132371	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3132386	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3135303	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3135315	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3135321	0.83[EUR][1000 genomes]
rs3135322	0.85[EUR][1000 genomes]
rs3135323	0.88[EUR][1000 genomes]
rs3135324	0.88[EUR][1000 genomes]
rs3135326	0.82[EUR][1000 genomes]
rs3135327	0.85[EUR][1000 genomes]
rs3135328	0.88[EUR][1000 genomes]
rs377392	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs381808	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs386628	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs393431	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs526983	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456857	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914955	0.81[ASN][1000 genomes]
rs763009	0.86[EUR][1000 genomes]
rs7755875	0.81[ASN][1000 genomes]
rs9257134	0.81[EUR][1000 genomes]
rs9257135	0.81[EUR][1000 genomes]
rs9257229	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1002925	ZSCAN23	cis	cerebellum	SCAN
rs1002925	ZSCAN16	cis	parietal	SCAN
rs1002925	ZNF323	cis	cerebellum	SCAN
rs1002925	HIST1H2BH	cis	cerebellum	SCAN
rs1002925	ZKSCAN3	cis	cerebellum	SCAN
rs1002925	ZNF323	cis	parietal	SCAN
rs1002925	NKAPL	cis	parietal	SCAN
rs1002925	ZSCAN23	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28800600-28801800	Weak transcription	K562	blood

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