Variant report

Variant	rs10405234
Chromosome Location	chr19:19756662-19756663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19756619-19757067	K562	blood:	n/a	n/a
2	POLR2A	chr19:19756618-19757169	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:19756619-19756963	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:19756552-19757509	HL-60	blood:	n/a	n/a
5	POLR2A	chr19:19756232-19757495	K562	blood:	n/a	n/a
6	POLR2A	chr19:19756620-19757579	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:19756660-19756897	K562	blood:	n/a	n/a
8	POLR2A	chr19:19756627-19757357	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr19:19756494-19757406	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:19756562-19757731	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:19756659-19756963	GM12891	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19751893..19756920-chr19:19758472..19762276,9	K562	blood:
2	chr19:19751259..19758144-chr19:19770384..19776332,14	K562	blood:
3	chr19:19746005..19749139-chr19:19754452..19756751,3	K562	blood:
4	chr19:19751259..19757786-chr19:19771999..19776232,8	K562	blood:
5	chr19:19754487..19757148-chr19:19764604..19766993,2	K562	blood:
6	chr19:19755727..19757407-chr19:19763663..19765667,2	MCF-7	breast:
7	chr19:19755704..19761642-chr19:19771468..19774473,6	MCF-7	breast:
8	chr19:19754977..19756747-chr19:19789710..19792104,2	K562	blood:

No data

Variant related genes	Relation type
GMIP	TF binding region
ENSG00000105726	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000181896	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10423311	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667828	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667844	0.86[EUR][1000 genomes]
rs11670710	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12974308	0.82[ASN][1000 genomes]
rs12976582	0.82[ASN][1000 genomes]
rs12982049	0.82[ASN][1000 genomes]
rs12982500	0.82[ASN][1000 genomes]
rs12983292	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1433079	0.98[ASN][1000 genomes]
rs16996227	0.82[ASN][1000 genomes]
rs2288865	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288867	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635562	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34558847	0.81[ASN][1000 genomes]
rs35035906	0.98[ASN][1000 genomes]
rs35445661	0.98[ASN][1000 genomes]
rs35449009	0.82[ASN][1000 genomes]
rs35792080	0.83[ASN][1000 genomes]
rs35801717	0.82[ASN][1000 genomes]
rs3752152	0.98[ASN][1000 genomes]
rs3794996	0.93[ASN][1000 genomes]
rs4808209	0.82[ASN][1000 genomes]
rs4808976	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249670	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251924	0.82[ASN][1000 genomes]
rs74181147	0.82[ASN][1000 genomes]
rs74181148	0.82[ASN][1000 genomes]
rs74181149	0.82[ASN][1000 genomes]
rs74181150	0.82[ASN][1000 genomes]
rs74181151	0.82[ASN][1000 genomes]
rs8107058	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv911310	chr19:19753882-19784891	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19754800-19757600	Weak transcription	NH-A	brain
2	chr19:19754800-19757800	Weak transcription	NHDF-Ad	bronchial
3	chr19:19754800-19761400	Weak transcription	HSMM	muscle
4	chr19:19754800-19763600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:19754800-19764200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:19754800-19767200	Weak transcription	Fetal Brain Male	brain
7	chr19:19754800-19769000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:19754800-19772400	Weak transcription	Right Atrium	heart
9	chr19:19755000-19756800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:19755000-19757000	Weak transcription	Stomach Mucosa	stomach
11	chr19:19755000-19759000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:19755000-19759000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:19755000-19759000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:19755000-19761800	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr19:19755000-19765600	Weak transcription	Hela-S3	cervix
16	chr19:19755000-19769600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:19755000-19770800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:19755000-19771000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:19755000-19771200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:19755000-19771200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:19755000-19772000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:19755000-19772000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:19755000-19772200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:19755200-19756800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr19:19755200-19757000	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:19755200-19757000	Strong transcription	K562	blood
27	chr19:19755200-19758600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:19755200-19758600	Strong transcription	Brain Angular Gyrus	brain
29	chr19:19755200-19759000	Strong transcription	Brain Hippocampus Middle	brain
30	chr19:19755200-19760200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:19755200-19761000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr19:19755200-19761200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:19755200-19761200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:19755200-19761200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:19755200-19761400	Strong transcription	Fetal Muscle Leg	muscle
36	chr19:19755200-19761600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:19755200-19761600	Strong transcription	Brain Anterior Caudate	brain
38	chr19:19755200-19761800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:19755200-19761800	Strong transcription	Brain Cingulate Gyrus	brain
40	chr19:19755200-19763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:19755200-19763400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:19755200-19763800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:19755200-19765800	Weak transcription	Fetal Kidney	kidney
44	chr19:19755200-19767200	Strong transcription	Fetal Brain Female	brain
45	chr19:19755200-19770600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:19755200-19770600	Strong transcription	Dnd41	blood
47	chr19:19755200-19770800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr19:19755200-19770800	Strong transcription	Adipose Nuclei	Adipose
49	chr19:19755200-19770800	Strong transcription	Brain Germinal Matrix	brain
50	chr19:19755200-19770800	Strong transcription	Fetal Intestine Large	intestine

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