Variant report

Variant	rs73551743
Chromosome Location	chr19:39645859-39645860
allele	C/G
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	SIN3AK20	chr19:39644790-39646296	MCF-7	breast:	n/a	n/a
2	GATA3	chr19:39645188-39645893	T-47D	breast:	n/a	chr19:39645214-39645224
3	NR2F2	chr19:39645072-39646001	MCF-7	breast:	n/a	n/a
4	MAX	chr19:39644653-39646265	MCF-7	breast:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
5	GATA3	chr19:39644826-39646058	MCF-7	breast:	n/a	chr19:39645214-39645224 chr19:39645069-39645079
6	ELF1	chr19:39644969-39645890	MCF-7	breast:	n/a	n/a
7	HDAC2	chr19:39645106-39646189	MCF-7	breast:	n/a	chr19:39645215-39645229 chr19:39645216-39645230 chr19:39645211-39645225
8	HDAC2	chr19:39644968-39645949	MCF-7	breast:	n/a	chr19:39645066-39645080 chr19:39645215-39645229 chr19:39645216-39645230 chr19:39645069-39645083 chr19:39645211-39645225 chr19:39645070-39645084
9	GATA3	chr19:39645064-39646018	MCF-7	breast:	n/a	chr19:39645214-39645224 chr19:39645069-39645079
10	ZNF217	chr19:39644954-39645879	MCF-7	breast:	n/a	n/a
11	MAX	chr19:39645192-39646062	MCF-7	breast:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
12	TCF12	chr19:39644861-39646241	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr19:39644670-39646174	MCF-7	breast:	n/a	n/a
14	MAX	chr19:39645066-39645888	ECC-1	luminal epithelium:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
15	NR2F2	chr19:39645183-39645923	MCF-7	breast:	n/a	n/a
16	GATA3	chr19:39645301-39646146	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39645610..39647317-chr19:39897484..39899400,2	MCF-7	breast:
2	chr19:39643758..39646287-chr19:39649616..39652008,3	K562	blood:
3	chr19:39612929..39614547-chr19:39644614..39646235,2	K562	blood:
4	chr19:39613047..39614883-chr19:39644735..39646568,2	K562	blood:
5	chr19:39643019..39646132-chr19:39671022..39674035,4	MCF-7	breast:
6	chr19:39522254..39524021-chr19:39644088..39646362,2	MCF-7	breast:
7	chr19:39644386..39647038-chr19:39665325..39668037,2	MCF-7	breast:
8	chr19:39645159..39645930-chr19:39677797..39678451,2	K562	blood:
9	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:
10	chr19:39643809..39645925-chr19:39673965..39675850,2	K562	blood:
11	chr19:39643041..39646015-chr19:39653933..39655727,2	K562	blood:
12	chr19:39620592..39621547-chr19:39645122..39646030,2	MCF-7	breast:

Variant related genes	Relation type
PAK4	TF binding region
ENSG00000269172	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000130669	Chromatin interaction
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11878229	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11878648	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879084	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879196	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880984	1.00[EUR][1000 genomes]
rs11881029	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882129	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882668	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882711	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882955	1.00[EUR][1000 genomes]
rs16973211	1.00[AMR][1000 genomes]
rs16973231	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57716250	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57769351	1.00[EUR][1000 genomes]
rs58626126	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58909586	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59303188	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60229944	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61641657	1.00[EUR][1000 genomes]
rs7246294	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7254424	1.00[EUR][1000 genomes]
rs7260015	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73549583	1.00[AMR][1000 genomes]
rs73549585	1.00[AMR][1000 genomes]
rs73549593	1.00[AMR][1000 genomes]
rs73549600	1.00[AMR][1000 genomes]
rs73551720	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551752	0.97[AFR][1000 genomes]
rs73551786	1.00[EUR][1000 genomes]
rs73553708	1.00[EUR][1000 genomes]
rs73553711	1.00[EUR][1000 genomes]
rs73553738	1.00[EUR][1000 genomes]
rs73553740	1.00[EUR][1000 genomes]
rs73553742	1.00[EUR][1000 genomes]
rs73930290	1.00[AMR][1000 genomes]
rs73930300	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73933809	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73933837	1.00[EUR][1000 genomes]
rs8101586	1.00[EUR][1000 genomes]
rs8111473	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:39624000-39647000	Weak transcription	NHLF	lung
5	chr19:39627200-39646800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:39630800-39646800	Weak transcription	Osteobl	bone
7	chr19:39630800-39651000	Weak transcription	NHDF-Ad	bronchial
8	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:39635400-39647000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:39635600-39647000	Weak transcription	NH-A	brain
11	chr19:39635600-39647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:39635800-39646000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr19:39636000-39647400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
15	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
16	chr19:39636800-39650800	Weak transcription	HUVEC	blood vessel
17	chr19:39637000-39653600	Weak transcription	Brain Germinal Matrix	brain
18	chr19:39637200-39647000	Weak transcription	Small Intestine	intestine
19	chr19:39637400-39647400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr19:39638000-39646000	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:39638000-39646800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:39638200-39648600	Weak transcription	Brain Angular Gyrus	brain
25	chr19:39640000-39646600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:39640000-39647600	Weak transcription	HSMMtube	muscle
27	chr19:39640000-39648400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
29	chr19:39640200-39646600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:39640200-39647400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:39640200-39647400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:39640200-39660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:39641000-39646200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:39641200-39649200	Weak transcription	Fetal Brain Female	brain
35	chr19:39641400-39646600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:39641800-39646400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:39642000-39649600	Enhancers	Placenta	Placenta
38	chr19:39642200-39646400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr19:39642200-39647400	Weak transcription	Right Atrium	heart
40	chr19:39642400-39646600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:39642400-39647000	Weak transcription	HSMM	muscle
42	chr19:39642400-39649000	Weak transcription	Thymus	Thymus
43	chr19:39642600-39646600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:39643400-39648200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:39644200-39646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:39644200-39646600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:39644200-39652200	Enhancers	Placenta Amnion	Placenta Amnion
48	chr19:39644400-39647400	Enhancers	Liver	Liver
49	chr19:39644400-39648800	Enhancers	Gastric	stomach
50	chr19:39644400-39649600	Enhancers	Pancreas	Pancrea

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