Variant report

Variant	rs11014389
Chromosome Location	chr10:25370796-25370797
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:25315162..25315967-chr10:25369953..25370895,6	MCF-7	breast:
2	chr10:25304800..25307444-chr10:25366624..25371121,4	MCF-7	breast:
3	chr10:25369500..25372471-chr10:25373482..25376338,3	MCF-7	breast:
4	chr10:25303695..25307800-chr10:25367762..25370827,4	K562	blood:
5	chr10:25304278..25309002-chr10:25368191..25372754,5	K562	blood:
6	chr10:25305403..25308444-chr10:25369519..25373361,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151023	Chromatin interaction
ENSG00000185875	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10828750	0.81[ASN][1000 genomes]
rs10828751	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10828752	0.86[ASN][1000 genomes]
rs10828754	0.81[ASN][1000 genomes]
rs10828755	0.83[ASN][1000 genomes]
rs11014365	0.82[CEU][hapmap]
rs11014367	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11014368	0.80[ASN][1000 genomes]
rs11014375	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11014379	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12219239	0.81[JPT][hapmap]
rs12414202	0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs12764623	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12773782	0.84[ASN][1000 genomes]
rs1492606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492607	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552770	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1552771	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2087781	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4508094	0.82[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4749004	0.84[ASN][1000 genomes]
rs4749005	0.83[ASN][1000 genomes]
rs902906	0.82[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs923757	0.88[ASN][1000 genomes]
rs923758	0.80[EUR][1000 genomes];0.84[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11014389	ENKUR	cis	parietal	SCAN
rs11014389	PIP4K2A	cis	parietal	SCAN
rs11014389	PTCHD3	cis	cerebellum	SCAN
rs11014389	THNSL1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25366000-25371200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:25367600-25374200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr10:25368400-25371400	Enhancers	HepG2	liver
4	chr10:25368400-25371800	Weak transcription	Left Ventricle	heart
5	chr10:25369400-25371000	Enhancers	Fetal Heart	heart
6	chr10:25369400-25373400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr10:25369400-25374000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:25369600-25371400	Enhancers	Brain Hippocampus Middle	brain
9	chr10:25369800-25370800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr10:25369800-25370800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr10:25369800-25370800	Enhancers	NH-A	brain
12	chr10:25369800-25371000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:25369800-25371000	Enhancers	Stomach Smooth Muscle	stomach
14	chr10:25369800-25371200	Enhancers	Fetal Lung	lung
15	chr10:25369800-25371400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:25369800-25372000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr10:25369800-25372000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr10:25369800-25372000	Enhancers	Colon Smooth Muscle	Colon
19	chr10:25369800-25373000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:25369800-25373000	Enhancers	Ovary	ovary
21	chr10:25369800-25373400	Enhancers	Brain Anterior Caudate	brain
22	chr10:25369800-25373400	Enhancers	Brain Cingulate Gyrus	brain
23	chr10:25369800-25373800	Enhancers	Brain Angular Gyrus	brain
24	chr10:25370000-25371000	Enhancers	Fetal Brain Male	brain
25	chr10:25370000-25371400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:25370000-25371400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:25370000-25374800	Weak transcription	K562	blood
28	chr10:25370200-25370800	Enhancers	Fetal Muscle Leg	muscle
29	chr10:25370200-25370800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr10:25370200-25371200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr10:25370400-25370800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:25370400-25370800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:25370400-25371000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr10:25370400-25371000	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr10:25370400-25371400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr10:25370400-25371400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr10:25370400-25371400	Weak transcription	Aorta	Aorta
38	chr10:25370400-25371600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr10:25370400-25371600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr10:25370400-25372000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr10:25370400-25372000	Enhancers	Osteobl	bone
42	chr10:25370600-25370800	Enhancers	Lung	lung
43	chr10:25370600-25372800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:25370600-25373000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr10:25370600-25374400	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links