Variant report

Variant	rs11084445
Chromosome Location	chr19:56823708-56823709
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	USF1	chr19:56823696-56823985	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF582-4	chr19:56823297-56823855	ENSG00000267298.1

Variant related genes	Relation type
ENSG00000267549	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10404293	0.85[CHD][hapmap]
rs10418888	0.83[CHD][hapmap];0.88[MEX][hapmap]
rs10424840	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11084444	0.81[CEU][hapmap];0.93[CHD][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11881864	0.81[CHD][hapmap]
rs11882259	0.85[CEU][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2869159	0.82[ASN][1000 genomes]
rs7252603	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107755	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv526325	chr19:56741186-56852035	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
7	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv1058026	chr19:56799847-56833153	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv1067261	chr19:56820571-56854916	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56772800-56824200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr19:56782800-56825200	Weak transcription	Psoas Muscle	Psoas
3	chr19:56783000-56825000	Weak transcription	Stomach Mucosa	stomach
4	chr19:56788200-56824400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:56789000-56823800	Weak transcription	Brain Angular Gyrus	brain
6	chr19:56799800-56825200	Weak transcription	Right Atrium	heart
7	chr19:56803000-56824200	Weak transcription	Fetal Thymus	thymus
8	chr19:56803200-56825000	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:56804400-56825000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:56804600-56825000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:56805200-56825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:56806000-56825000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:56806400-56825200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:56806400-56825200	Weak transcription	Brain Hippocampus Middle	brain
15	chr19:56806400-56825200	Weak transcription	NH-A	brain
16	chr19:56806600-56825000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:56807000-56825200	Weak transcription	NHLF	lung
18	chr19:56807600-56823800	Weak transcription	GM12878-XiMat	blood
19	chr19:56807800-56825000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:56807800-56825200	Weak transcription	Brain Germinal Matrix	brain
21	chr19:56807800-56825200	Weak transcription	Colonic Mucosa	Colon
22	chr19:56807800-56825200	Weak transcription	Esophagus	oesophagus
23	chr19:56808200-56825000	Weak transcription	HMEC	breast
24	chr19:56810000-56825200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:56813600-56825000	Weak transcription	Fetal Heart	heart
26	chr19:56813600-56825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:56813600-56825200	Weak transcription	Left Ventricle	heart
28	chr19:56813800-56825000	Weak transcription	HUVEC	blood vessel
29	chr19:56814000-56825200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:56814200-56825000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:56814200-56825200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:56814400-56824800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:56814400-56825000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:56814400-56825200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:56814400-56825200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr19:56814400-56825400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:56814600-56825000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr19:56815400-56825000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:56815600-56825000	Weak transcription	HSMMtube	muscle
40	chr19:56815600-56825200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:56816200-56825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:56816400-56825000	Weak transcription	Brain Substantia Nigra	brain
43	chr19:56816400-56825200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr19:56816800-56825000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr19:56817200-56824200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:56817400-56823800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:56817400-56825200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:56817600-56823800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr19:56817600-56824200	Weak transcription	Lung	lung
50	chr19:56817600-56824400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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