Variant report

Variant	rs4517466
Chromosome Location	chr10:52366952-52366953
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr10:52366500-52367089	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
2	chr10:52366580..52370875-chr10:52371309..52374318,4	K562	blood:
3	chr10:52365691..52371767-chr10:52381261..52385919,7	K562	blood:
4	chr10:52363969..52366872-chr10:52366929..52369870,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230036	TF binding region
ENSG00000230036	Chromatin interaction
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11006277	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006436	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006438	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17497903	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4367895	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4475874	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4503481	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4636605	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4935738	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61857061	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61858140	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858144	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858145	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858147	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858148	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858149	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858152	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61858153	0.99[ASN][1000 genomes]
rs7919879	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4517466	FLJ31958	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
2	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:52358400-52367000	Enhancers	Fetal Lung	lung
4	chr10:52358800-52367800	Enhancers	Brain Hippocampus Middle	brain
5	chr10:52359400-52369200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr10:52360200-52375600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr10:52361600-52369000	Enhancers	Brain Anterior Caudate	brain
8	chr10:52362000-52368400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr10:52362000-52368400	Enhancers	Brain Substantia Nigra	brain
10	chr10:52362200-52367400	Enhancers	Brain Cingulate Gyrus	brain
11	chr10:52362200-52372400	Weak transcription	Esophagus	oesophagus
12	chr10:52362400-52367200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr10:52362600-52368800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr10:52362800-52368000	Enhancers	HepG2	liver
15	chr10:52363000-52368000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr10:52363200-52368000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:52363200-52368000	Enhancers	Stomach Mucosa	stomach
18	chr10:52363200-52371600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr10:52363200-52372000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr10:52363400-52368000	Enhancers	Colon Smooth Muscle	Colon
21	chr10:52363800-52367800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr10:52364000-52367200	Enhancers	Right Ventricle	heart
23	chr10:52364000-52367600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr10:52364000-52369800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr10:52364200-52368400	Enhancers	Duodenum Mucosa	Duodenum
26	chr10:52364200-52370000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr10:52364400-52372000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr10:52364400-52374400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr10:52365000-52368800	Enhancers	Fetal Heart	heart
30	chr10:52365000-52368800	Weak transcription	Thymus	Thymus
31	chr10:52365000-52369800	Weak transcription	Gastric	stomach
32	chr10:52365000-52369800	Weak transcription	Right Atrium	heart
33	chr10:52365000-52371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr10:52365200-52367000	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr10:52365200-52367600	Enhancers	NHLF	lung
36	chr10:52365200-52368200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr10:52365200-52368200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr10:52365200-52369600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr10:52365200-52374000	Weak transcription	Placenta	Placenta
40	chr10:52365400-52367200	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr10:52365400-52367400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr10:52365400-52367400	Enhancers	Hela-S3	cervix
43	chr10:52365400-52367600	Enhancers	NHDF-Ad	bronchial
44	chr10:52365400-52367600	Enhancers	Osteobl	bone
45	chr10:52365400-52368200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr10:52365400-52368200	Weak transcription	Fetal Muscle Leg	muscle
47	chr10:52365400-52369000	Enhancers	Liver	Liver
48	chr10:52365400-52370200	Weak transcription	Fetal Thymus	thymus
49	chr10:52365400-52370200	Weak transcription	Spleen	Spleen
50	chr10:52365400-52370800	Weak transcription	Lung	lung

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