Variant report

Variant	rs10422570
Chromosome Location	chr19:39864236-39864237
allele	A/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	POLR2A	chr19:39850716-39886400	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39863959-39864292	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:39864016-39864344	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39863292..39866130-chr19:39896253..39898902,2	MCF-7	breast:

Variant related genes	Relation type
SAMD4B	TF binding region
ENSG00000128016	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10405369	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422996	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424274	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13344909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13346452	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28519468	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
5	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
7	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
9	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:39839200-39879200	Strong transcription	Dnd41	blood
12	chr19:39841600-39880000	Strong transcription	Fetal Intestine Large	intestine
13	chr19:39842000-39880000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:39842200-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:39842200-39880400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr19:39842400-39880400	Strong transcription	Thymus	Thymus
17	chr19:39842600-39880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:39848200-39880000	Weak transcription	Fetal Heart	heart
19	chr19:39850400-39881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr19:39851600-39866400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr19:39851800-39867600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr19:39852800-39880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:39854000-39866200	Weak transcription	Stomach Mucosa	stomach
24	chr19:39854000-39876000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:39855000-39865600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:39856200-39864400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:39856600-39880200	Strong transcription	Fetal Thymus	thymus
28	chr19:39857200-39875600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr19:39857200-39880200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:39857200-39880400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:39857400-39875000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:39857400-39875200	Strong transcription	Primary B cells from cord blood	blood
33	chr19:39858800-39865200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr19:39858800-39872600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:39858800-39879600	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr19:39859000-39864600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:39859000-39864800	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr19:39859000-39875400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr19:39859000-39880200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:39859400-39864800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:39860000-39875000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr19:39860000-39880400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:39860800-39875800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:39861200-39865400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr19:39861400-39866600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr19:39861600-39865000	Weak transcription	GM12878-XiMat	blood
47	chr19:39861600-39866600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:39861600-39868800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:39861800-39865200	Genic enhancers	NHLF	lung
50	chr19:39861800-39866600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links