Variant report

Variant	rs12436555
Chromosome Location	chr14:24634825-24634826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:24633164-24636338	GM12878	blood:	n/a	n/a
2	POLR2A	chr14:24629795-24635666	GM12891	blood:	n/a	n/a
3	POLR2A	chr14:24633525-24635479	GM12878	blood:	n/a	n/a
4	POLR2A	chr14:24633713-24635401	GM19193	blood:	n/a	n/a
5	POLR2A	chr14:24633055-24635512	GM12892	blood:	n/a	n/a
6	POLR2A	chr14:24633800-24634917	GM19099	blood:	n/a	n/a
7	POLR2A	chr14:24628953-24638117	GM12892	blood:	n/a	n/a
8	POLR2A	chr14:24633576-24635017	GM12878	blood:	n/a	n/a
9	POLR2A	chr14:24633740-24635004	GM12878	blood:	n/a	n/a
10	POU2F2	chr14:24634545-24634874	GM12891	blood:	n/a	n/a
11	POLR2A	chr14:24633065-24635506	GM18505	blood:	n/a	n/a
12	POLR2A	chr14:24634040-24635055	GM12891	blood:	n/a	n/a
13	POLR2A	chr14:24633241-24636356	GM12878	blood:	n/a	n/a
14	POLR2A	chr14:24629025-24642975	GM12878	blood:	n/a	n/a
15	POLR2A	chr14:24629878-24635641	GM12891	blood:	n/a	n/a
16	POLR2A	chr14:24632955-24635559	GM12891	blood:	n/a	n/a
17	POLR2A	chr14:24628755-24643416	GM12878	blood:	n/a	n/a
18	POLR2A	chr14:24628891-24643060	GM12892	blood:	n/a	n/a
19	POLR2A	chr14:24634146-24635590	K562	blood:	n/a	n/a
20	POLR2A	chr14:24628761-24637814	GM12892	blood:	n/a	n/a
21	POLR2A	chr14:24634814-24634993	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr14:24633204-24636364	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24629652..24632387-chr14:24633563..24637546,5	K562	blood:
2	chr14:24631619..24637585-chr14:24644952..24647499,6	K562	blood:
3	chr14:24630385..24632878-chr14:24633609..24637546,6	K562	blood:
4	chr14:24631879..24637788-chr14:24639506..24644553,5	K562	blood:
5	chr14:24634478..24636921-chr14:24656618..24658137,2	K562	blood:
6	chr14:24627382..24636644-chr14:24680297..24686914,11	MCF-7	breast:
7	chr14:24634103..24636921-chr14:24656610..24658137,3	K562	blood:

No data

Variant related genes	Relation type
IRF9	TF binding region
ENSG00000213920	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000213928	Chromatin interaction
ENSG00000100918	Chromatin interaction
ENSG00000260669	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10583	1.00[CEU][hapmap]
rs12432194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3405661	chr14:24189883-24670942	Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	esv1827678	chr14:24520544-24663325	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv869985	chr14:24578013-24652669	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv901498	chr14:24591892-24662177	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12436555	RABGGTA	cis	temporal cortex	BrainEAC

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24631000-24640600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:24631200-24640600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr14:24631400-24635400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:24631400-24635400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr14:24631600-24636200	Strong transcription	Fetal Brain Female	brain
6	chr14:24631600-24637200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:24631600-24637200	Strong transcription	A549	lung
8	chr14:24631600-24640400	Weak transcription	Fetal Brain Male	brain
9	chr14:24631600-24653800	Weak transcription	K562	blood
10	chr14:24631800-24635400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr14:24631800-24636200	Strong transcription	Brain Germinal Matrix	brain
12	chr14:24632000-24635400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr14:24632000-24635400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr14:24632000-24635400	Strong transcription	HMEC	breast
15	chr14:24632000-24635600	Strong transcription	HSMM	muscle
16	chr14:24632000-24636000	Strong transcription	HUVEC	blood vessel
17	chr14:24632000-24636200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr14:24632000-24636600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr14:24632000-24637200	Strong transcription	Fetal Lung	lung
20	chr14:24632000-24637200	Strong transcription	HepG2	liver
21	chr14:24632000-24639200	Strong transcription	Osteobl	bone
22	chr14:24632200-24636200	Strong transcription	NH-A	brain
23	chr14:24632200-24636600	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr14:24632200-24637200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:24632200-24637200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr14:24632200-24637200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr14:24632200-24637200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr14:24632200-24637200	Strong transcription	Aorta	Aorta
29	chr14:24632200-24637200	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr14:24632200-24637200	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr14:24632200-24637400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr14:24632200-24640000	Strong transcription	Thymus	Thymus
33	chr14:24632400-24635000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr14:24632400-24635200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr14:24632400-24636400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr14:24632400-24637000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr14:24632400-24637000	Strong transcription	HSMMtube	muscle
38	chr14:24632400-24637200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr14:24632400-24637200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr14:24632400-24637200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr14:24632400-24637200	Strong transcription	NHLF	lung
42	chr14:24632400-24639800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr14:24632400-24639800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:24632600-24635200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr14:24632600-24635400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr14:24632600-24635400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr14:24632600-24635600	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr14:24632600-24635600	Strong transcription	Dnd41	blood
49	chr14:24632600-24635800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr14:24632600-24636200	Strong transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links