Variant report

Variant	rs601966
Chromosome Location	chr19:39533819-39533820
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	chr19:39519101..39521598-chr19:39532998..39534703,2	K562	blood:

Variant related genes	Relation type
ENSG00000267992	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10410965	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11666514	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12150941	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1268240	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1268251	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12978285	0.82[ASN][1000 genomes]
rs1672647	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1672649	0.86[AMR][1000 genomes]
rs2012598	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2081994	0.84[ASN][1000 genomes]
rs2081995	0.84[ASN][1000 genomes]
rs2318895	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2318896	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2873835	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2873836	0.81[ASN][1000 genomes]
rs34640039	0.81[ASN][1000 genomes]
rs472104	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs473729	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs473878	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.90[ASN][1000 genomes]
rs476616	0.92[ASN][1000 genomes]
rs479001	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802004	0.81[ASN][1000 genomes]
rs4802012	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803179	0.84[ASN][1000 genomes]
rs4803180	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803184	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs485226	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs497378	0.90[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs533573	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs536244	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs580494	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs586059	0.90[ASN][1000 genomes]
rs600128	0.82[ASN][1000 genomes]
rs603268	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629685	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs631879	0.92[ASN][1000 genomes]
rs631952	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs646580	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs650450	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672576	0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7247817	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7254745	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7258182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73043568	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73047946	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103036	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8103319	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8105050	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8109914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][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	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2760517	chr19:39530012-39544234	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv526711	chr19:39533754-39538592	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv458570	chr19:39533754-39538592	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv579507	chr19:39533754-39538592	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs601966	ZNF526	cis	parietal	SCAN
rs601966	ATP5SL	cis	cerebellum	SCAN
rs601966	PTGIR	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39523400-39535400	Weak transcription	Right Atrium	heart
2	chr19:39530800-39543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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