Variant report

Variant	rs10413140
Chromosome Location	chr19:39914028-39914029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39913659-39914570	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:39913199-39917525	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
4	REST	chr19:39913255-39914116	H1-neurons	neurons:	n/a	n/a
5	REST	chr19:39913175-39917362	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:39913941-39914246	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:39914010-39914031	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:39913886-39914619	K562	blood:	n/a	n/a
10	POLR2A	chr19:39913999-39914647	A549	lung:	n/a	n/a
11	SIN3AK20	chr19:39913141-39929158	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr19:39913889-39914694	K562	blood:	n/a	n/a
13	POLR2A	chr19:39913839-39917581	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:39913942-39914556	A549	lung:	n/a	n/a
15	POLR2A	chr19:39913308-39917626	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39911800..39914936-chr19:39915871..39918478,3	MCF-7	breast:
2	chr19:39911856..39914486-chr19:39957675..39960546,2	K562	blood:
3	chr19:39913480..39916274-chr19:39975273..39977291,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269410	TF binding region
PLEKHG2	TF binding region
ENSG00000269410	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000196235	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10408589	1.00[EUR][1000 genomes]
rs10409917	1.00[EUR][1000 genomes]
rs10413673	1.00[EUR][1000 genomes]
rs10415077	1.00[EUR][1000 genomes]
rs10415279	1.00[EUR][1000 genomes]
rs13346052	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2230765	1.00[EUR][1000 genomes]
rs4100178	1.00[EUR][1000 genomes]
rs61569178	1.00[AMR][1000 genomes]
rs6508847	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	1.00[AMR][1000 genomes]
rs73549928	1.00[AMR][1000 genomes]
rs73549930	1.00[AMR][1000 genomes]
rs73549931	1.00[AMR][1000 genomes]
rs73551806	1.00[AMR][1000 genomes]
rs73551815	1.00[AMR][1000 genomes]
rs73551829	1.00[AMR][1000 genomes]
rs73551839	1.00[AMR][1000 genomes]
rs73551844	1.00[AMR][1000 genomes]
rs7359872	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
7	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
8	nsv911688	chr19:39891219-39919538	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
9	esv1832456	chr19:39901611-39914748	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	45 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39904800-39921000	Weak transcription	Small Intestine	intestine
2	chr19:39904800-39925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39905000-39921200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:39905200-39916600	Weak transcription	Brain Hippocampus Middle	brain
5	chr19:39905200-39916600	Weak transcription	Brain Substantia Nigra	brain
6	chr19:39905200-39918800	Weak transcription	Pancreas	Pancrea
7	chr19:39905400-39916000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:39905400-39921200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:39905400-39921200	Weak transcription	K562	blood
10	chr19:39905400-39923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:39905600-39916400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:39905600-39921600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr19:39905800-39915600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:39905800-39915600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:39905800-39917000	Strong transcription	Thymus	Thymus
16	chr19:39905800-39918000	Weak transcription	HepG2	liver
17	chr19:39905800-39923000	Weak transcription	Brain Anterior Caudate	brain
18	chr19:39905800-39923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:39906200-39914200	Weak transcription	Esophagus	oesophagus
20	chr19:39906200-39915000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:39906200-39916000	Strong transcription	Fetal Intestine Small	intestine
22	chr19:39906200-39919000	Weak transcription	HMEC	breast
23	chr19:39906400-39915400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr19:39906400-39915400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:39906400-39916200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:39906400-39916800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:39906400-39917200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr19:39906400-39921200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr19:39906600-39916600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:39906600-39916600	Strong transcription	Fetal Thymus	thymus
31	chr19:39906600-39916800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:39906800-39916600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr19:39906800-39916600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:39906800-39916800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:39907000-39914600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:39907000-39915600	Strong transcription	Dnd41	blood
37	chr19:39907000-39915800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:39907000-39916600	Strong transcription	Fetal Brain Female	brain
39	chr19:39907000-39917200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:39907000-39919000	Weak transcription	Right Atrium	heart
41	chr19:39907200-39916800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:39907200-39917200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:39907400-39915400	Strong transcription	Adipose Nuclei	Adipose
44	chr19:39907400-39915600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr19:39907400-39915600	Strong transcription	A549	lung
46	chr19:39907400-39916000	Strong transcription	NHLF	lung
47	chr19:39907400-39916200	Strong transcription	Stomach Smooth Muscle	stomach
48	chr19:39907400-39916400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:39907600-39915400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:39907600-39916000	Strong transcription	Right Ventricle	heart

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