Variant report

Variant	rs13023016
Chromosome Location	chr2:113378875-113378876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113344897..113346779-chr2:113377975..113380310,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243389	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1053652	0.83[CHB][hapmap]
rs10758	0.83[CHB][hapmap]
rs11676691	0.88[EUR][1000 genomes]
rs11677284	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678996	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11680446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12476928	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12479380	0.85[CHB][hapmap]
rs13387435	0.80[CHB][hapmap]
rs3088301	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35743012	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4368335	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs4547533	0.80[EUR][1000 genomes]
rs4848284	0.81[EUR][1000 genomes]
rs4849078	0.84[EUR][1000 genomes]
rs4849079	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4849083	0.81[EUR][1000 genomes]
rs4849084	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849086	0.89[CHB][hapmap]
rs62158654	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6542074	0.83[CHB][hapmap]
rs6705487	0.83[CHB][hapmap]
rs6724434	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs908545	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13023016	IL1A	cis	cerebellum	SCAN
rs13023016	LOC654433	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113348600-113383600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:113349000-113384000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:113357800-113384200	Weak transcription	Pancreas	Pancrea
4	chr2:113358000-113384000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:113370400-113383800	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:113371600-113382000	Weak transcription	Spleen	Spleen
7	chr2:113372200-113379800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:113372200-113384200	Weak transcription	Fetal Intestine Small	intestine
9	chr2:113372400-113384000	Weak transcription	Brain Anterior Caudate	brain
10	chr2:113372400-113388600	Weak transcription	Gastric	stomach
11	chr2:113372600-113379800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:113372800-113388000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:113373000-113379800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:113373000-113379800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:113373000-113383200	Weak transcription	Fetal Brain Female	brain
16	chr2:113373200-113384000	Weak transcription	Brain Germinal Matrix	brain
17	chr2:113376600-113379800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:113376800-113379600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:113377400-113384200	Weak transcription	Right Atrium	heart
20	chr2:113377800-113379600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:113378200-113382000	Weak transcription	Adipose Nuclei	Adipose
22	chr2:113378400-113379800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:113378400-113379800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:113378400-113382200	Enhancers	HMEC	breast
25	chr2:113378600-113379400	Enhancers	NHEK	skin
26	chr2:113378600-113379600	Enhancers	Hela-S3	cervix
27	chr2:113378600-113380200	Enhancers	NHDF-Ad	bronchial
28	chr2:113378600-113380400	Enhancers	NHLF	lung
29	chr2:113378600-113381600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:113378800-113379000	Enhancers	H9 Cell Line	embryonic stem cell
31	chr2:113378800-113379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:113378800-113379600	Enhancers	NH-A	brain
33	chr2:113378800-113379600	Enhancers	Osteobl	bone
34	chr2:113378800-113379800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:113378800-113382000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:113378800-113384000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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