Variant report

Variant	rs73549912
Chromosome Location	chr19:39933616-39933617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39933105-39933616	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39933009-39933656	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:39933302-39933734	HCT-116	colon:	n/a	n/a
5	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39921621..39923975-chr19:39932520..39935648,3	MCF-7	breast:
2	chr19:39917343..39919360-chr19:39932932..39935140,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPS16-1	chr19:39932509-39936109	NONHSAT066299

No data

Variant related genes	Relation type
SUPT5H	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10413140	1.00[AMR][1000 genomes]
rs13346052	1.00[AMR][1000 genomes]
rs61569178	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547970	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547976	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547991	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547993	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547999	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549905	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549906	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549922	1.00[AMR][1000 genomes]
rs73549928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551806	1.00[AMR][1000 genomes]
rs73551815	1.00[AMR][1000 genomes]
rs73551829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551844	1.00[AMR][1000 genomes]
rs7359872	1.00[AFR][1000 genomes];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	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39926600-39935200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:39927400-39935200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39927400-39935200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:39927400-39935200	Weak transcription	Gastric	stomach
5	chr19:39927400-39935200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:39927600-39934800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:39927600-39935000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:39927600-39935000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:39927600-39935000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:39927600-39935000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:39927600-39935000	Weak transcription	HMEC	breast
12	chr19:39927600-39935200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr19:39927600-39935200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:39927600-39935200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr19:39927600-39935200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr19:39927600-39935200	Weak transcription	Brain Anterior Caudate	brain
17	chr19:39927600-39935200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr19:39927600-39935200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr19:39927600-39935200	Weak transcription	Fetal Kidney	kidney
20	chr19:39927600-39935200	Weak transcription	HSMMtube	muscle
21	chr19:39927600-39935200	Weak transcription	NHLF	lung
22	chr19:39928600-39935000	Weak transcription	Fetal Intestine Small	intestine
23	chr19:39929400-39935000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:39929400-39935000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr19:39929800-39934000	Weak transcription	Placenta	Placenta
26	chr19:39929800-39935000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:39929800-39935000	Weak transcription	NHEK	skin
28	chr19:39930600-39935000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:39931200-39935200	Weak transcription	Brain Angular Gyrus	brain
30	chr19:39931200-39935200	Weak transcription	GM12878-XiMat	blood
31	chr19:39931400-39934600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:39931400-39934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:39931400-39935000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:39931400-39935000	Weak transcription	Primary B cells from cord blood	blood
35	chr19:39931400-39935000	Weak transcription	Fetal Stomach	stomach
36	chr19:39931400-39935000	Weak transcription	Hela-S3	cervix
37	chr19:39931400-39935200	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:39931400-39935200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:39931400-39935200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr19:39931800-39934800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:39931800-39935000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:39931800-39935200	Weak transcription	Liver	Liver
43	chr19:39932000-39935000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:39932000-39935200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr19:39932200-39934600	Weak transcription	Dnd41	blood
46	chr19:39932200-39935000	Weak transcription	HepG2	liver
47	chr19:39932400-39934800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:39932400-39935000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:39932400-39935200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:39932600-39935000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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