Variant report

Variant	rs12252715
Chromosome Location	chr10:25369955-25369956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:25315371..25316092-chr10:25369588..25370596,3	K562	blood:
2	chr10:25315162..25315967-chr10:25369953..25370895,6	MCF-7	breast:
3	chr10:25079435..25081057-chr10:25368417..25370064,2	K562	blood:
4	chr10:24931513..24932500-chr10:25369531..25370644,4	K562	blood:
5	chr10:25304800..25307444-chr10:25366624..25371121,4	MCF-7	breast:
6	chr10:25369500..25372471-chr10:25373482..25376338,3	MCF-7	breast:
7	chr10:25016699..25017443-chr10:25369664..25370556,4	K562	blood:
8	chr10:24906446..24907157-chr10:25369477..25370117,2	MCF-7	breast:
9	chr10:25303695..25307800-chr10:25367762..25370827,4	K562	blood:
10	chr10:25304278..25309002-chr10:25368191..25372754,5	K562	blood:
11	chr10:25305403..25308444-chr10:25369519..25373361,4	MCF-7	breast:
12	chr10:25315173..25316027-chr10:25369505..25370579,6	MCF-7	breast:
13	chr10:25357593..25359343-chr10:25368933..25370472,2	K562	blood:
14	chr10:25369667..25370602-chr10:25971300..25972009,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185875	Chromatin interaction
ENSG00000151023	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10508683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014380	1.00[ASN][1000 genomes]
rs11014386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014391	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252765	1.00[CEU][hapmap]
rs12255476	0.81[AFR][1000 genomes]
rs12258541	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12266610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266753	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2148208	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs56140300	1.00[ASN][1000 genomes]
rs72780394	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72780398	1.00[ASN][1000 genomes]
rs7901590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550224	chr10:25335854-25385858	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1036683	chr10:25337592-25398119	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv894969	chr10:25345720-25395579	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25365400-25370400	Enhancers	Fetal Intestine Large	intestine
2	chr10:25365400-25370400	Enhancers	Fetal Intestine Small	intestine
3	chr10:25366000-25371200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:25367400-25370000	Enhancers	K562	blood
5	chr10:25367600-25374200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:25368400-25370400	Enhancers	Duodenum Mucosa	Duodenum
7	chr10:25368400-25370400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr10:25368400-25371400	Enhancers	HepG2	liver
9	chr10:25368400-25371800	Weak transcription	Left Ventricle	heart
10	chr10:25369000-25370400	Enhancers	Liver	Liver
11	chr10:25369200-25370600	Enhancers	Stomach Mucosa	stomach
12	chr10:25369200-25370600	Enhancers	A549	lung
13	chr10:25369400-25370400	Enhancers	Small Intestine	intestine
14	chr10:25369400-25371000	Enhancers	Fetal Heart	heart
15	chr10:25369400-25373400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr10:25369400-25374000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:25369600-25370000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr10:25369600-25370000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
19	chr10:25369600-25370000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr10:25369600-25370000	Weak transcription	NHLF	lung
21	chr10:25369600-25370400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr10:25369600-25370400	Enhancers	Fetal Kidney	kidney
23	chr10:25369600-25371400	Enhancers	Brain Hippocampus Middle	brain
24	chr10:25369800-25370000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:25369800-25370000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr10:25369800-25370000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:25369800-25370000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr10:25369800-25370000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:25369800-25370000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:25369800-25370000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:25369800-25370000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr10:25369800-25370000	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr10:25369800-25370000	Enhancers	NHDF-Ad	bronchial
34	chr10:25369800-25370200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr10:25369800-25370400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr10:25369800-25370400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr10:25369800-25370400	Enhancers	Brain Germinal Matrix	brain
38	chr10:25369800-25370400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr10:25369800-25370400	Enhancers	Hela-S3	cervix
40	chr10:25369800-25370400	Enhancers	HMEC	breast
41	chr10:25369800-25370400	Enhancers	NHEK	skin
42	chr10:25369800-25370400	Flanking Active TSS	Osteobl	bone
43	chr10:25369800-25370800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:25369800-25370800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr10:25369800-25370800	Enhancers	NH-A	brain
46	chr10:25369800-25371000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr10:25369800-25371000	Enhancers	Stomach Smooth Muscle	stomach
48	chr10:25369800-25371200	Enhancers	Fetal Lung	lung
49	chr10:25369800-25371400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr10:25369800-25372000	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links