Variant report

Variant	rs10142080
Chromosome Location	chr14:24639842-24639843
allele	C/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:5)
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	chr14:24639375-24643075	GM12891	blood:	n/a	n/a
2	POLR2A	chr14:24639429-24641812	GM12891	blood:	n/a	n/a
3	POLR2A	chr14:24639600-24639879	GM12878	blood:	n/a	n/a
4	POLR2A	chr14:24639439-24639896	GM12891	blood:	n/a	n/a
5	POLR2A	chr14:24639637-24639891	GM12878	blood:	n/a	n/a
6	POLR2A	chr14:24638137-24643601	GM12892	blood:	n/a	n/a
7	POLR2A	chr14:24639415-24643065	GM12892	blood:	n/a	n/a
8	POLR2A	chr14:24639366-24643007	GM12892	blood:	n/a	n/a
9	POLR2A	chr14:24639650-24639991	GM12878	blood:	n/a	n/a
10	POLR2A	chr14:24639327-24639946	GM12891	blood:	n/a	n/a
11	POLR2A	chr14:24639824-24640832	HepG2	liver:	n/a	n/a
12	POLR2A	chr14:24629025-24642975	GM12878	blood:	n/a	n/a
13	POLR2A	chr14:24628755-24643416	GM12878	blood:	n/a	n/a
14	POLR2A	chr14:24628891-24643060	GM12892	blood:	n/a	n/a
15	POLR2A	chr14:24635678-24642994	GM12891	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24631879..24637788-chr14:24639506..24644553,5	K562	blood:
2	chr14:24582038..24584525-chr14:24638691..24642019,3	MCF-7	breast:
3	chr14:24639747..24642550-chr14:24651922..24653711,2	K562	blood:
4	chr14:24628913..24631680-chr14:24639494..24642572,3	K562	blood:
5	chr14:24562783..24564737-chr14:24638245..24640098,2	K562	blood:

No data

Variant related genes	Relation type
REC8	TF binding region
ENSG00000100897	Chromatin interaction
ENSG00000129535	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000092098	Chromatin interaction
ENSG00000213928	Chromatin interaction
ENSG00000100889	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10131288	1.00[ASN][1000 genomes]
rs10132189	1.00[ASN][1000 genomes]
rs10136993	1.00[ASN][1000 genomes]
rs10140260	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142310	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10143943	1.00[ASN][1000 genomes]
rs10144791	1.00[ASN][1000 genomes]
rs10146665	1.00[ASN][1000 genomes]
rs17101758	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28373297	1.00[EUR][1000 genomes]
rs28396996	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28435365	1.00[ASN][1000 genomes]
rs28533649	1.00[ASN][1000 genomes]
rs28589355	1.00[ASN][1000 genomes]
rs28636804	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470080	1.00[ASN][1000 genomes]
rs7151467	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005722	1.00[ASN][1000 genomes]
rs8008047	1.00[ASN][1000 genomes]
rs8011199	1.00[ASN][1000 genomes]
rs8012049	1.00[ASN][1000 genomes]
rs8019514	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

No data

Chromatin state (count:122 , 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	chr14:24631600-24640400	Weak transcription	Fetal Brain Male	brain
4	chr14:24631600-24653800	Weak transcription	K562	blood
5	chr14:24632200-24640000	Strong transcription	Thymus	Thymus
6	chr14:24632600-24640400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr14:24634400-24640000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr14:24634400-24640200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:24634600-24640600	Weak transcription	Fetal Kidney	kidney
10	chr14:24634600-24641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr14:24634800-24640600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:24635200-24640200	Strong transcription	Fetal Muscle Leg	muscle
13	chr14:24635200-24640600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr14:24635200-24647400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr14:24635400-24640200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr14:24635400-24640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:24635400-24640600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr14:24635400-24640600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr14:24635400-24640600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr14:24635400-24640800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr14:24635400-24641200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr14:24635400-24647800	Weak transcription	HMEC	breast
23	chr14:24635600-24640600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr14:24635600-24640800	Weak transcription	Fetal Heart	heart
25	chr14:24635600-24647000	Weak transcription	Dnd41	blood
26	chr14:24636000-24640800	Weak transcription	HUVEC	blood vessel
27	chr14:24636200-24640200	Weak transcription	Brain Germinal Matrix	brain
28	chr14:24636200-24640600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr14:24636200-24640600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr14:24636200-24640600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr14:24636200-24640600	Weak transcription	Brain Angular Gyrus	brain
32	chr14:24636200-24640600	Weak transcription	Fetal Brain Female	brain
33	chr14:24636200-24640800	Weak transcription	NH-A	brain
34	chr14:24636200-24646000	Weak transcription	Stomach Mucosa	stomach
35	chr14:24636400-24640200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr14:24636400-24640200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr14:24636400-24640600	Weak transcription	Brain Hippocampus Middle	brain
38	chr14:24636400-24640600	Weak transcription	Right Ventricle	heart
39	chr14:24636400-24640800	Weak transcription	Psoas Muscle	Psoas
40	chr14:24636600-24642200	Weak transcription	Hela-S3	cervix
41	chr14:24636600-24646000	Weak transcription	Small Intestine	intestine
42	chr14:24636600-24647400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr14:24637000-24640600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr14:24637000-24640600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr14:24637000-24640600	Weak transcription	Esophagus	oesophagus
46	chr14:24637000-24640800	Weak transcription	Ovary	ovary
47	chr14:24637000-24648000	Weak transcription	HSMM	muscle
48	chr14:24637000-24648200	Weak transcription	HSMMtube	muscle
49	chr14:24637200-24640400	Weak transcription	Brain Anterior Caudate	brain
50	chr14:24637200-24640400	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links