Variant report

Variant	rs581486
Chromosome Location	chr19:56668436-56668437
allele	A/C
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	ELF1	chr19:56668142-56668440	GM12878	blood:	n/a	chr19:56668279-56668290
2	POLR2A	chr19:56668411-56668677	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:56668309-56668782	K562	blood:	n/a	n/a
4	POLR2A	chr19:56668266-56668567	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56662631..56664494-chr19:56667011..56669719,2	K562	blood:

Variant related genes	Relation type
ZNF444	TF binding region
ENSG00000204533	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs2631642	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631652	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs274141	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs274144	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs274145	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274146	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs274151	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs274154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs274155	0.87[CHB][hapmap]
rs274156	0.89[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs274159	0.90[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs274163	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs274165	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs274167	0.83[EUR][1000 genomes]
rs274180	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs274182	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3103059	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3103060	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs480528	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs481291	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs482506	0.85[ASN][1000 genomes]
rs487922	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs488118	0.85[ASN][1000 genomes]
rs488196	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs565171	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61283021	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs650832	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs651800	0.85[ASN][1000 genomes]
rs652204	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs671061	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs679082	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs901476	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS 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	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
12	nsv528361	chr19:56638845-56688570	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56653800-56669200	Weak transcription	HSMM	muscle
2	chr19:56653800-56669400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr19:56653800-56673000	Weak transcription	Hela-S3	cervix
4	chr19:56653800-56674000	Weak transcription	Fetal Kidney	kidney
5	chr19:56654000-56681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:56654200-56674000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:56654400-56671200	Weak transcription	Small Intestine	intestine
8	chr19:56655200-56672200	Weak transcription	NHDF-Ad	bronchial
9	chr19:56656400-56672200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:56659200-56673000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr19:56659400-56671000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:56659600-56670400	Weak transcription	NHEK	skin
13	chr19:56660200-56670400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:56661400-56676200	Weak transcription	Fetal Brain Male	brain
15	chr19:56661600-56669200	Weak transcription	Brain Angular Gyrus	brain
16	chr19:56662000-56672200	Weak transcription	Fetal Heart	heart
17	chr19:56663000-56673200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:56663200-56674000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr19:56663800-56672400	Strong transcription	Dnd41	blood
20	chr19:56663800-56673000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:56663800-56673600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:56664000-56672800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:56664000-56673000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:56664400-56670200	Weak transcription	NH-A	brain
25	chr19:56664600-56668800	Strong transcription	Aorta	Aorta
26	chr19:56664600-56672800	Strong transcription	Fetal Intestine Large	intestine
27	chr19:56664800-56672800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:56664800-56673800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:56664800-56673800	Strong transcription	Fetal Intestine Small	intestine
30	chr19:56665000-56668800	Genic enhancers	Pancreas	Pancrea
31	chr19:56665000-56670200	Weak transcription	Colon Smooth Muscle	Colon
32	chr19:56665000-56674000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:56665200-56672400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:56665200-56673400	Strong transcription	Gastric	stomach
35	chr19:56665200-56674000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:56665200-56674400	Strong transcription	Fetal Stomach	stomach
37	chr19:56665400-56668600	Strong transcription	Brain Anterior Caudate	brain
38	chr19:56665400-56668600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr19:56665400-56671000	Strong transcription	Fetal Lung	lung
40	chr19:56665400-56672800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:56665400-56673200	Weak transcription	HUVEC	blood vessel
42	chr19:56665400-56674000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:56665400-56674200	Strong transcription	Fetal Brain Female	brain
44	chr19:56665600-56672600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr19:56665600-56672800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:56665600-56673200	Strong transcription	Thymus	Thymus
47	chr19:56665600-56673400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:56665800-56673000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:56665800-56674200	Strong transcription	Brain Germinal Matrix	brain
50	chr19:56666000-56668800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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