Variant report

Variant	rs30458
Chromosome Location	chr19:39835498-39835499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39832559..39836457-chr19:39880660..39884768,5	MCF-7	breast:
2	chr19:39834979..39837753-chr19:39902595..39905469,2	MCF-7	breast:
3	chr19:39834449..39837367-chr19:39853608..39855481,2	K562	blood:
4	chr19:39672992..39674987-chr19:39833706..39835660,2	K562	blood:
5	chr19:39835239..39836908-chr19:39924259..39926190,2	MCF-7	breast:
6	chr19:39832709..39837239-chr19:39925090..39928725,4	K562	blood:
7	chr19:39835229..39838232-chr19:39847109..39849134,3	MCF-7	breast:
8	chr19:39830669..39836861-chr19:39895802..39900887,6	MCF-7	breast:
9	chr19:39835028..39836930-chr19:39843586..39846123,3	MCF-7	breast:
10	chr19:39835368..39837206-chr19:39838321..39840003,3	MCF-7	breast:
11	chr19:39834302..39836305-chr19:39857341..39859446,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000179134	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000063322	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs251905	0.82[EUR][1000 genomes]
rs251907	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28370340	0.81[ASN][1000 genomes]
rs30453	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30454	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30455	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36264	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36266	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36270	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs40441	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45601936	0.81[ASN][1000 genomes]
rs562638	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685125	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7246750	0.81[ASN][1000 genomes]
rs7250420	0.81[ASN][1000 genomes]
rs8102194	0.81[ASN][1000 genomes]
rs917319	0.81[ASN][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	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
7	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
8	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834000-39835800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr19:39834000-39842400	Weak transcription	Gastric	stomach
3	chr19:39834200-39835800	Enhancers	Primary hematopoietic stem cells	blood
4	chr19:39834200-39835800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr19:39834200-39835800	Weak transcription	Left Ventricle	heart
6	chr19:39834200-39835800	Weak transcription	Spleen	Spleen
7	chr19:39834200-39836000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:39834200-39836200	Enhancers	Duodenum Mucosa	Duodenum
9	chr19:39834200-39836200	Enhancers	K562	blood
10	chr19:39834200-39836400	Weak transcription	Aorta	Aorta
11	chr19:39834200-39836800	Enhancers	Right Ventricle	heart
12	chr19:39834200-39838400	Weak transcription	Ovary	ovary
13	chr19:39834200-39846600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr19:39834400-39835600	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr19:39834400-39835600	Weak transcription	Right Atrium	heart
17	chr19:39834400-39835600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr19:39834400-39835600	Genic enhancers	A549	lung
19	chr19:39834400-39835800	Enhancers	Brain Germinal Matrix	brain
20	chr19:39834400-39835800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr19:39834400-39835800	Enhancers	Stomach Smooth Muscle	stomach
22	chr19:39834400-39835800	Enhancers	HepG2	liver
23	chr19:39834400-39836000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr19:39834400-39836000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr19:39834400-39836000	Enhancers	Brain Substantia Nigra	brain
26	chr19:39834400-39836000	Enhancers	Fetal Lung	lung
27	chr19:39834400-39836200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr19:39834400-39836400	Weak transcription	Pancreas	Pancrea
29	chr19:39834400-39836600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:39834400-39836600	Enhancers	Brain Cingulate Gyrus	brain
31	chr19:39834400-39836800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:39834400-39837000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr19:39834400-39837000	Weak transcription	Fetal Thymus	thymus
34	chr19:39834400-39837200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr19:39834400-39837200	Weak transcription	HSMMtube	muscle
36	chr19:39834400-39837600	Weak transcription	NH-A	brain
37	chr19:39834400-39838200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:39834400-39838200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr19:39834400-39838400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:39834400-39839800	Enhancers	Fetal Heart	heart
41	chr19:39834400-39840600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:39834400-39841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:39834400-39841800	Weak transcription	Lung	lung
44	chr19:39834400-39842000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr19:39834400-39842000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr19:39834400-39842000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:39834400-39842200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:39834400-39842200	Weak transcription	Esophagus	oesophagus
49	chr19:39834400-39842400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr19:39834400-39844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links