Variant report

Variant	rs73551844
Chromosome Location	chr19:39983576-39983577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39925083..39926660-chr19:39982191..39985073,2	K562	blood:
2	chr19:39982701..39986911-chr19:39987055..39990908,4	MCF-7	breast:
3	chr19:39930044..39931944-chr19:39980921..39983797,2	MCF-7	breast:
4	chr19:39975925..39978735-chr19:39983543..39985534,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIMM50-1	chr19:39982152-39984422	NONHSAT066304

Variant related genes	Relation type
ENSG00000213922	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10413140	1.00[AMR][1000 genomes]
rs13346052	1.00[AMR][1000 genomes]
rs13346478	1.00[EUR][1000 genomes]
rs60840261	1.00[EUR][1000 genomes]
rs61569178	1.00[AMR][1000 genomes]
rs7247534	1.00[EUR][1000 genomes]
rs7254051	1.00[EUR][1000 genomes]
rs73547970	1.00[AMR][1000 genomes]
rs73547976	1.00[AMR][1000 genomes]
rs73547991	1.00[AMR][1000 genomes]
rs73547993	1.00[AMR][1000 genomes]
rs73547999	1.00[AMR][1000 genomes]
rs73549905	1.00[AMR][1000 genomes]
rs73549906	1.00[AMR][1000 genomes]
rs73549912	1.00[AMR][1000 genomes]
rs73549922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549928	1.00[AMR][1000 genomes]
rs73549930	1.00[AMR][1000 genomes]
rs73549931	1.00[AMR][1000 genomes]
rs73551806	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551829	1.00[AMR][1000 genomes]
rs73551839	1.00[AMR][1000 genomes]
rs73553808	1.00[EUR][1000 genomes]
rs73553810	1.00[EUR][1000 genomes]
rs73553830	1.00[EUR][1000 genomes]
rs73553832	1.00[EUR][1000 genomes]
rs73553833	1.00[EUR][1000 genomes]
rs7359872	1.00[AMR][1000 genomes]
rs8101134	1.00[EUR][1000 genomes]
rs9676712	1.00[EUR][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	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39972200-39986400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39972800-39983600	Strong transcription	Fetal Stomach	stomach
3	chr19:39972800-39984200	Weak transcription	Stomach Mucosa	stomach
4	chr19:39972800-39988600	Weak transcription	Right Atrium	heart
5	chr19:39973000-39983800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:39973200-39983800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:39973200-39983800	Strong transcription	Fetal Muscle Leg	muscle
8	chr19:39973400-39983800	Strong transcription	Brain Germinal Matrix	brain
9	chr19:39973600-39988400	Weak transcription	Fetal Brain Male	brain
10	chr19:39973800-39983800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:39976200-39983600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:39979800-39983600	Weak transcription	Hela-S3	cervix
13	chr19:39980000-39984400	Weak transcription	NHDF-Ad	bronchial
14	chr19:39980000-39988600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr19:39980600-39988600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:39980800-39986600	Weak transcription	NHLF	lung
17	chr19:39980800-39988200	Weak transcription	HUVEC	blood vessel
18	chr19:39980800-39988400	Weak transcription	K562	blood
19	chr19:39981000-39983800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:39981000-39985000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:39981000-39985200	Weak transcription	Brain Substantia Nigra	brain
22	chr19:39981000-39985400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:39981000-39985600	Weak transcription	Esophagus	oesophagus
24	chr19:39981000-39986200	Weak transcription	HepG2	liver
25	chr19:39981000-39986600	Weak transcription	NH-A	brain
26	chr19:39981000-39988200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:39981000-39988400	Weak transcription	Aorta	Aorta
28	chr19:39981000-39988400	Weak transcription	GM12878-XiMat	blood
29	chr19:39981000-39988400	Weak transcription	HSMMtube	muscle
30	chr19:39981000-39988600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:39981000-39988600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr19:39981000-39988600	Weak transcription	Gastric	stomach
33	chr19:39981000-39988800	Weak transcription	Pancreas	Pancrea
34	chr19:39981200-39984200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr19:39981200-39985000	Weak transcription	Right Ventricle	heart
36	chr19:39981200-39985200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:39981200-39985200	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:39981200-39985600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:39981200-39985800	Weak transcription	Lung	lung
40	chr19:39981200-39986000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr19:39981200-39988400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr19:39981400-39983600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr19:39981400-39983600	Weak transcription	HMEC	breast
44	chr19:39981400-39983800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:39981400-39983800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr19:39981400-39984600	Weak transcription	Colon Smooth Muscle	Colon
47	chr19:39981400-39984600	Weak transcription	Small Intestine	intestine
48	chr19:39981400-39985200	Weak transcription	Brain Angular Gyrus	brain
49	chr19:39981400-39985200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr19:39981400-39985400	Weak transcription	Fetal Lung	lung

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