Variant report

Variant	rs1564206
Chromosome Location	chr19:38040076-38040077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38039837-38040235	HL-60	blood:	n/a	n/a
2	CTCF	chr19:38039940-38040090	GM12865	blood:	n/a	n/a

Variant related genes	Relation type
ZNF540	TF binding region
ZNF571-AS1	TF binding region
ENSG00000180458	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10402671	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10403173	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10404031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10406379	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10408619	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10409605	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10410588	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10412510	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10412786	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10417576	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10420268	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10420552	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425795	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083432	0.87[EUR][1000 genomes]
rs12459015	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12979640	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13744	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1531549	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1564208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958861	0.89[EUR][1000 genomes]
rs16958863	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1975937	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1975939	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075284	0.84[EUR][1000 genomes]
rs2287229	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2291002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28512414	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909093	0.81[EUR][1000 genomes]
rs2909102	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2909105	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2927739	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2927740	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2927742	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2927746	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2927747	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2972430	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2972434	0.80[EUR][1000 genomes]
rs2972446	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2972447	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2972458	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3101746	0.85[EUR][1000 genomes]
rs3101747	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3112434	0.81[EUR][1000 genomes]
rs35863684	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3829688	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802024	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802029	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803215	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803231	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803233	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803262	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803263	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803276	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803287	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6508736	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8100646	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8103647	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8110865	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9304568	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs954504	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs958305	0.85[EUR][1000 genomes]
rs968073	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9749368	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9797618	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9941475	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv2478	chr19:38025340-38043818	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1564206	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38029800-38042000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:38032400-38080800	ZNF genes & repeats	Liver	Liver
3	chr19:38032600-38075200	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:38035000-38042800	ZNF genes & repeats	Brain Hippocampus Middle	brain
5	chr19:38036600-38041800	ZNF genes & repeats	Fetal Lung	lung
6	chr19:38037800-38042800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
7	chr19:38037800-38043000	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:38037800-38043200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:38037800-38043800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
10	chr19:38037800-38045400	ZNF genes & repeats	Brain Anterior Caudate	brain
11	chr19:38038000-38041800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:38038000-38042400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
13	chr19:38038000-38042600	ZNF genes & repeats	Brain Angular Gyrus	brain
14	chr19:38038000-38042800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
15	chr19:38038000-38042800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
16	chr19:38038000-38043000	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr19:38038000-38078400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:38038600-38042800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:38038600-38042800	ZNF genes & repeats	Brain Substantia Nigra	brain
20	chr19:38038600-38079600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
21	chr19:38038800-38045600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:38039000-38042800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:38039000-38043000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:38039200-38042800	ZNF genes & repeats	Esophagus	oesophagus
25	chr19:38039200-38043000	ZNF genes & repeats	Thymus	Thymus
26	chr19:38039400-38042200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:38039400-38042800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:38039400-38042800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:38039400-38042800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:38039600-38042800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
31	chr19:38039800-38042600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:38039800-38042600	ZNF genes & repeats	Fetal Brain Male	brain
33	chr19:38039800-38042800	ZNF genes & repeats	Gastric	stomach
34	chr19:38039800-38043000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:38040000-38042800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:38040000-38042800	ZNF genes & repeats	Colonic Mucosa	Colon

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