Variant report

Variant	rs7543124
Chromosome Location	chr1:48227135-48227136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1077842	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1561573	0.80[YRI][hapmap]
rs3844086	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][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	nsv829760	chr1:48111126-48308188	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv871257	chr1:48111699-48334490	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv871175	chr1:48150309-48254782	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1001126	chr1:48164622-48320862	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1003161	chr1:48207715-48286563	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7543124	GPBP1L1	cis	cerebellum	SCAN
rs7543124	C1orf223	cis	cerebellum	SCAN
rs7543124	DMAP1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:48215400-48236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:48218600-48228400	Weak transcription	Lung	lung
3	chr1:48218600-48239800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:48222400-48231800	Weak transcription	Pancreas	Pancrea
5	chr1:48224400-48228200	Weak transcription	Esophagus	oesophagus
6	chr1:48224400-48230400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:48225400-48231600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:48225400-48234000	Enhancers	Right Atrium	heart
9	chr1:48225600-48230000	Weak transcription	Fetal Intestine Small	intestine
10	chr1:48225600-48237000	Weak transcription	Fetal Intestine Large	intestine
11	chr1:48225800-48228600	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:48226000-48227200	Enhancers	Fetal Muscle Leg	muscle
13	chr1:48226400-48228200	Enhancers	Spleen	Spleen
14	chr1:48226600-48227200	Enhancers	Aorta	Aorta
15	chr1:48226600-48227600	Enhancers	Fetal Lung	lung
16	chr1:48226600-48227600	Enhancers	Placenta	Placenta
17	chr1:48226600-48231600	Weak transcription	Brain Germinal Matrix	brain
18	chr1:48226800-48228600	Enhancers	GM12878-XiMat	blood
19	chr1:48227000-48227200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
20	chr1:48227000-48233600	Weak transcription	Hela-S3	cervix

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