Variant report

Variant	rs62119697
Chromosome Location	chr19:39855737-39855738
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39850716-39886400	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39853890..39856826-chr19:39881619..39883140,2	MCF-7	breast:
2	chr19:39855111..39857327-chr19:39867163..39868939,2	MCF-7	breast:
3	chr19:39854636..39857180-chr19:39900646..39903469,2	MCF-7	breast:
4	chr19:39848239..39850464-chr19:39853560..39855951,2	MCF-7	breast:
5	chr19:39855401..39857094-chr19:39901000..39902939,2	MCF-7	breast:
6	chr19:39853372..39857037-chr19:39858264..39860770,3	MCF-7	breast:

No data

Variant related genes	Relation type
SAMD4B	TF binding region
RN7SL566P	TF binding region
ENSG00000006712	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000241983	Chromatin interaction
ENSG00000179134	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs40469	0.82[EUR][1000 genomes]
rs45591338	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs45613331	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61736260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62119675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62122887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122891	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	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
7	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
6	chr19:39836400-39862600	Strong transcription	Duodenum Mucosa	Duodenum
7	chr19:39836600-39864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
10	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr19:39837600-39863600	Strong transcription	Fetal Intestine Small	intestine
12	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
13	chr19:39838200-39858200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:39838200-39858200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:39838200-39862600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:39839000-39857600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:39839000-39858200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:39839200-39879200	Strong transcription	Dnd41	blood
21	chr19:39841600-39880000	Strong transcription	Fetal Intestine Large	intestine
22	chr19:39842000-39864200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr19:39842000-39880000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:39842200-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:39842200-39880400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr19:39842400-39856600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:39842400-39862400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:39842400-39880400	Strong transcription	Thymus	Thymus
29	chr19:39842600-39880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:39844400-39857800	Strong transcription	Fetal Lung	lung
31	chr19:39847400-39864000	Strong transcription	Primary hematopoietic stem cells	blood
32	chr19:39848200-39880000	Weak transcription	Fetal Heart	heart
33	chr19:39848400-39864200	Strong transcription	K562	blood
34	chr19:39849000-39860200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr19:39850400-39881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr19:39851400-39856200	Weak transcription	Fetal Brain Male	brain
37	chr19:39851400-39861000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:39851600-39859200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:39851600-39862800	Weak transcription	Small Intestine	intestine
40	chr19:39851600-39866400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr19:39851800-39859200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:39851800-39859600	Weak transcription	Pancreas	Pancrea
43	chr19:39851800-39860200	Weak transcription	Gastric	stomach
44	chr19:39851800-39860800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr19:39851800-39867600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr19:39852400-39858000	Genic enhancers	Brain Cingulate Gyrus	brain
47	chr19:39852600-39856600	Genic enhancers	Brain Anterior Caudate	brain
48	chr19:39852800-39855800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:39852800-39856200	Enhancers	Psoas Muscle	Psoas
50	chr19:39852800-39856800	Genic enhancers	Fetal Muscle Trunk	muscle

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