Variant report

Variant	rs2454013
Chromosome Location	chr8:104154713-104154714
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104152186..104155681-chr8:104309748..104312108,3	MCF-7	breast:
2	chr8:104153176..104156099-chr8:104164228..104166566,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164929	Chromatin interaction
ENSG00000247081	Chromatin interaction
ENSG00000164930	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10088491	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10955310	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12056711	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs13259545	0.82[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs13264626	0.81[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1494276	0.83[YRI][hapmap]
rs1497449	0.92[ASN][1000 genomes]
rs1497450	0.91[JPT][hapmap]
rs1497451	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1497452	0.87[ASN][1000 genomes]
rs1845430	0.81[ASN][1000 genomes]
rs1846063	0.86[JPT][hapmap]
rs1846064	0.87[ASN][1000 genomes]
rs1976326	0.81[ASN][1000 genomes]
rs2132867	0.81[ASN][1000 genomes]
rs2249240	0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2249255	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2249256	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2256164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454000	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2454001	0.81[ASN][1000 genomes]
rs2454002	0.81[ASN][1000 genomes]
rs2454003	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2454004	0.81[ASN][1000 genomes]
rs2454006	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2454012	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2454014	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454032	0.91[JPT][hapmap]
rs2454033	0.91[JPT][hapmap]
rs2454036	0.91[JPT][hapmap]
rs2454037	0.91[JPT][hapmap]
rs2454038	0.91[JPT][hapmap]
rs2515175	0.91[JPT][hapmap]
rs2515181	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2515184	0.87[ASN][1000 genomes]
rs2515185	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2515186	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2515190	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2935579	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3019158	0.91[JPT][hapmap]
rs3019159	0.91[JPT][hapmap]
rs4734071	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4734687	0.91[JPT][hapmap]
rs4734689	0.92[ASN][1000 genomes]
rs4734690	0.92[ASN][1000 genomes]
rs7001897	0.92[ASN][1000 genomes]
rs7014418	0.91[ASN][1000 genomes]
rs953253	0.80[ASN][1000 genomes]
rs991312	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[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	nsv831413	chr8:104085141-104269789	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2454013	CD248	trans	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104152200-104155600	Active TSS	Brain Substantia Nigra	brain
2	chr8:104152600-104155000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr8:104152800-104156000	Active TSS	Brain Angular Gyrus	brain
4	chr8:104153000-104154800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr8:104153200-104154800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr8:104153200-104156000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr8:104153400-104155000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr8:104153600-104155000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:104153600-104155400	Weak transcription	Aorta	Aorta
10	chr8:104153600-104156200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr8:104153600-104159000	Weak transcription	Spleen	Spleen
12	chr8:104153800-104155000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr8:104153800-104161200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr8:104154000-104154800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:104154000-104154800	Active TSS	Adipose Nuclei	Adipose
16	chr8:104154000-104155000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr8:104154000-104155600	Enhancers	NH-A	brain
18	chr8:104154000-104159800	Weak transcription	Pancreas	Pancrea
19	chr8:104154000-104177200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr8:104154200-104155000	Flanking Active TSS	Fetal Brain Female	brain
21	chr8:104154200-104155600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:104154200-104155800	Flanking Active TSS	Osteobl	bone
23	chr8:104154200-104160800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:104154400-104154800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr8:104154400-104154800	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr8:104154400-104155200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:104154600-104154800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr8:104154600-104154800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
29	chr8:104154600-104155000	Active TSS	NHLF	lung
30	chr8:104154600-104155200	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr8:104154600-104155200	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr8:104154600-104155200	Enhancers	Fetal Brain Male	brain
33	chr8:104154600-104155200	Flanking Active TSS	NHDF-Ad	bronchial
34	chr8:104154600-104156000	Enhancers	Muscle Satellite Cultured Cells	--

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