Variant report

Variant	rs10402565
Chromosome Location	chr19:41122068-41122069
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41121824-41122243	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:41122046-41122201	K562	blood:	n/a	n/a
3	POLR2A	chr19:41121670-41122104	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:41119264..41121274-chr19:41121495..41123120,2	MCF-7	breast:
2	chr19:41118984..41122545-chr19:41130944..41134653,3	MCF-7	breast:
3	chr19:41120433..41122395-chr19:41149709..41152254,3	MCF-7	breast:
4	chr19:41121010..41122780-chr19:41313951..41315644,2	MCF-7	breast:
5	chr19:41119884..41122816-chr19:41127370..41130174,2	MCF-7	breast:
6	chr19:41117621..41122754-chr19:41128365..41133445,15	K562	blood:

No data

Variant related genes	Relation type
LTBP4	TF binding region
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10408452	1.00[AMR][1000 genomes]
rs10408716	1.00[AMR][1000 genomes]
rs10415973	1.00[AMR][1000 genomes]
rs10417139	1.00[AMR][1000 genomes]
rs10422737	1.00[AMR][1000 genomes]
rs12104289	1.00[AMR][1000 genomes]
rs13347002	1.00[AMR][1000 genomes]
rs183852	1.00[AMR][1000 genomes]
rs187908	1.00[AMR][1000 genomes]
rs268658	1.00[AMR][1000 genomes]
rs268660	1.00[AMR][1000 genomes]
rs268661	1.00[AMR][1000 genomes]
rs268665	1.00[AMR][1000 genomes]
rs268667	1.00[AMR][1000 genomes]
rs268675	1.00[AMR][1000 genomes]
rs268681	1.00[AMR][1000 genomes]
rs28368968	1.00[AMR][1000 genomes]
rs28636772	1.00[AMR][1000 genomes]
rs4150994	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
13	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
16	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41109800-41122600	Weak transcription	Aorta	Aorta
3	chr19:41116600-41137000	Weak transcription	Psoas Muscle	Psoas
4	chr19:41117000-41140200	Weak transcription	Brain Angular Gyrus	brain
5	chr19:41117400-41125200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr19:41120200-41127800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:41120400-41127000	Weak transcription	Brain Germinal Matrix	brain
8	chr19:41120400-41139800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:41120600-41125400	Weak transcription	Gastric	stomach
10	chr19:41120600-41129400	Weak transcription	Pancreas	Pancrea
11	chr19:41120600-41133000	Weak transcription	Fetal Brain Male	brain
12	chr19:41120800-41123000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:41120800-41125200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:41120800-41127200	Weak transcription	Fetal Brain Female	brain
15	chr19:41120800-41128000	Weak transcription	Primary B cells from cord blood	blood
16	chr19:41120800-41128000	Weak transcription	Small Intestine	intestine
17	chr19:41120800-41139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr19:41120800-41140200	Weak transcription	Brain Anterior Caudate	brain
19	chr19:41121000-41122200	Enhancers	Colonic Mucosa	Colon
20	chr19:41121000-41122200	Enhancers	Duodenum Mucosa	Duodenum
21	chr19:41121000-41122200	Genic enhancers	HMEC	breast
22	chr19:41121000-41122200	Enhancers	NHDF-Ad	bronchial
23	chr19:41121000-41122600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:41121000-41122800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:41121000-41123200	Genic enhancers	Fetal Lung	lung
26	chr19:41121000-41124600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr19:41121000-41124800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:41121000-41125000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:41121000-41125000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:41121000-41125000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:41121000-41125200	Weak transcription	Primary T cells from cord blood	blood
32	chr19:41121000-41125200	Weak transcription	Fetal Thymus	thymus
33	chr19:41121000-41125200	Weak transcription	Left Ventricle	heart
34	chr19:41121000-41125200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:41121000-41125200	Weak transcription	Stomach Mucosa	stomach
36	chr19:41121000-41125200	Weak transcription	A549	lung
37	chr19:41121000-41125400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr19:41121000-41125400	Weak transcription	Esophagus	oesophagus
39	chr19:41121000-41125600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:41121000-41125600	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:41121000-41129400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr19:41121200-41122200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:41121200-41122200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:41121200-41122200	Genic enhancers	Fetal Intestine Small	intestine
45	chr19:41121200-41122200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr19:41121200-41122800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:41121200-41122800	Weak transcription	Right Ventricle	heart
48	chr19:41121200-41123200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:41121200-41124400	Weak transcription	Ovary	ovary
50	chr19:41121200-41125200	Weak transcription	H9 Cell Line	embryonic stem cell

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