Variant report

Variant	rs12545793
Chromosome Location	chr8:99061992-99061993
allele	G/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	FOSL2	chr8:99061911-99062274	SK-N-SH	brain:	n/a	n/a
2	FOS	chr8:99061976-99062109	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:98879599..98882619-chr8:99058852..99062253,4	MCF-7	breast:
2	chr8:99053215..99055370-chr8:99061297..99063461,2	K562	blood:
3	chr8:99056634..99059248-chr8:99059651..99063296,8	MCF-7	breast:
4	chr8:99056304..99059597-chr8:99060333..99064411,5	K562	blood:

Variant related genes	Relation type
RPL30	TF binding region
ENSG00000207067	Chromatin interaction
ENSG00000156482	Chromatin interaction
ENSG00000132561	Chromatin interaction
ENSG00000245970	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2444860	0.87[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4735522	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62523598	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[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	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription 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	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv465745	chr8:99061992-99116201	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv611805	chr8:99061992-99116201	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12545793	LAPTM4B	cis	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99059000-99063400	Weak transcription	Brain Angular Gyrus	brain
2	chr8:99059200-99062000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr8:99059200-99062000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:99059200-99062000	Weak transcription	Right Ventricle	heart
5	chr8:99059200-99062000	Weak transcription	HSMM	muscle
6	chr8:99059200-99062200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr8:99059200-99062400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:99059200-99062600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:99059200-99062800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr8:99059200-99063000	Weak transcription	GM12878-XiMat	blood
11	chr8:99059200-99063200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr8:99059200-99063200	Weak transcription	Fetal Kidney	kidney
13	chr8:99059200-99063400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:99059200-99063400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr8:99059200-99064000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr8:99059200-99064200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr8:99059200-99065000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr8:99059200-99066200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr8:99059200-99070800	Weak transcription	A549	lung
20	chr8:99059200-99071000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr8:99059400-99062000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr8:99059400-99062000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr8:99059400-99062200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr8:99059400-99062800	Weak transcription	Pancreas	Pancrea
25	chr8:99059400-99063200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr8:99059400-99063200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr8:99059400-99063600	Weak transcription	Fetal Intestine Large	intestine
28	chr8:99059400-99063600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr8:99059400-99064600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr8:99059400-99076200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr8:99059600-99064400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr8:99060000-99064200	Weak transcription	Fetal Intestine Small	intestine
33	chr8:99060800-99064600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr8:99060800-99065000	Weak transcription	Liver	Liver
35	chr8:99061200-99063000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:99061400-99062800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:99061800-99062000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr8:99061800-99062200	Enhancers	NHDF-Ad	bronchial
39	chr8:99061800-99062200	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links