Variant report

Variant	rs73546026
Chromosome Location	chr19:39810058-39810059
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	MXI1	chr19:39809950-39811697	SK-N-SH	brain:	n/a	n/a
2	REST	chr19:39808605-39811614	PANC-1	pancreas:	n/a	chr19:39808983-39808996 chr19:39809350-39809364 chr19:39808986-39808999 chr19:39810047-39810057 chr19:39808979-39808999 chr19:39808979-39808999
3	MYC	chr19:39810018-39810169	GM12878	blood:	n/a	n/a
4	RUNX3	chr19:39809927-39810258	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:39810050-39810133	K562	blood:	n/a	n/a
6	BCL3	chr19:39809571-39810514	A549	lung:	n/a	n/a
7	SIN3AK20	chr19:39808138-39811714	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39803732..39806747-chr19:39808288..39811295,3	MCF-7	breast:
2	chr19:39684826..39687710-chr19:39809011..39811329,2	K562	blood:
3	chr19:39809900..39813494-chr19:39831059..39834441,3	MCF-7	breast:
4	chr19:39807609..39810419-chr19:39829994..39832837,2	MCF-7	breast:

Variant related genes	Relation type
LRFN1	TF binding region
ENSG00000130755	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000188505	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000128011	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs56222183	1.00[AMR][1000 genomes]
rs57536536	1.00[AMR][1000 genomes]
rs58949744	1.00[AMR][1000 genomes]
rs60577443	1.00[AMR][1000 genomes]
rs60840261	1.00[AMR][1000 genomes]
rs61112725	1.00[AMR][1000 genomes]
rs61124676	1.00[AMR][1000 genomes]
rs61213828	1.00[AMR][1000 genomes]
rs61595075	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61730567	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250234	1.00[AMR][1000 genomes]
rs7250913	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73544098	1.00[AMR][1000 genomes]
rs73546015	1.00[AMR][1000 genomes]
rs73546080	1.00[AMR][1000 genomes]
rs73547904	1.00[AMR][1000 genomes]
rs73547972	1.00[AMR][1000 genomes]
rs73553808	1.00[AMR][1000 genomes]
rs73553810	1.00[AMR][1000 genomes]
rs73553812	1.00[AMR][1000 genomes]
rs73553822	1.00[AMR][1000 genomes]
rs73553830	1.00[AMR][1000 genomes]
rs73553832	1.00[AMR][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	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833830	chr19:39709538-39837846	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
4	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
6	nsv911681	chr19:39797716-39856246	Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39798600-39810800	Weak transcription	Right Atrium	heart
2	chr19:39798800-39810600	Weak transcription	Primary B cells from cord blood	blood
3	chr19:39799000-39810400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:39799200-39810200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:39800000-39810200	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:39800400-39810200	Weak transcription	Fetal Lung	lung
7	chr19:39800600-39811000	Weak transcription	Small Intestine	intestine
8	chr19:39801400-39810400	Weak transcription	Brain Substantia Nigra	brain
9	chr19:39801400-39810600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:39802600-39810800	Weak transcription	Right Ventricle	heart
11	chr19:39803000-39810600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:39803600-39810200	Weak transcription	Colonic Mucosa	Colon
13	chr19:39804600-39810600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:39805000-39810200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr19:39805600-39810200	Weak transcription	Fetal Muscle Leg	muscle
16	chr19:39805600-39810400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:39805800-39810800	Weak transcription	Liver	Liver
18	chr19:39806000-39810200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:39806000-39810400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr19:39806000-39810400	Weak transcription	Ovary	ovary
21	chr19:39806000-39810600	Weak transcription	Lung	lung
22	chr19:39806000-39810800	Weak transcription	Esophagus	oesophagus
23	chr19:39806200-39810200	Weak transcription	Fetal Thymus	thymus
24	chr19:39806200-39810600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:39806600-39810600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr19:39806800-39810200	Weak transcription	Fetal Stomach	stomach
27	chr19:39807000-39810200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr19:39807000-39810400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:39807200-39810200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr19:39807600-39810200	Weak transcription	A549	lung
31	chr19:39808200-39810200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:39809200-39810200	Weak transcription	Primary T cells from cord blood	blood
33	chr19:39809200-39810400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:39809600-39810400	Enhancers	Pancreas	Pancrea
35	chr19:39809600-39810600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:39809600-39811000	Enhancers	Spleen	Spleen
37	chr19:39809600-39811200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:39809600-39811200	Enhancers	Fetal Heart	heart
39	chr19:39809800-39810200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
40	chr19:39809800-39810200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr19:39809800-39810200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:39809800-39810200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr19:39809800-39810400	Enhancers	Primary T cells fromperipheralblood	blood
44	chr19:39809800-39810400	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr19:39809800-39810600	Flanking Active TSS	Fetal Brain Female	brain
46	chr19:39809800-39810600	Flanking Active TSS	K562	blood
47	chr19:39809800-39810800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:39809800-39810800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr19:39809800-39810800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr19:39809800-39810800	Active TSS	Brain Inferior Temporal Lobe	brain

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