Variant report

Variant	rs2597553
Chromosome Location	chr4:121786273-121786274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10857073	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10857074	0.84[EUR][1000 genomes]
rs1397767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs2102551	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2251270	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667170	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2667192	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3114953	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343173	0.86[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs343176	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs343177	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343183	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs343191	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4833673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6828945	0.85[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846000	0.87[AMR][1000 genomes]
rs72680456	0.87[AFR][1000 genomes]
rs843557	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs907295	0.83[EUR][1000 genomes]
rs907297	0.87[CEU][hapmap]
rs9991423	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1013704	chr4:121657648-121791601	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv4490	chr4:121782939-121801246	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2597553	PRDM5	cis	Whole Blood	GTEx
rs2597553	QRFPR	cis	cerebellum	SCAN
rs2597553	SYNPO2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121765800-121786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:121766000-121786600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:121766200-121790800	Weak transcription	Ovary	ovary
4	chr4:121771800-121786800	Weak transcription	Fetal Lung	lung
5	chr4:121775200-121790800	Weak transcription	Fetal Kidney	kidney
6	chr4:121779800-121786400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:121780000-121786600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:121780200-121786800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:121780200-121790600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:121780600-121787000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:121783800-121786400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:121784200-121798000	Weak transcription	Fetal Intestine Small	intestine
13	chr4:121784600-121791200	Weak transcription	Pancreas	Pancrea
14	chr4:121786000-121787400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:121786000-121787600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:121786200-121787000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr4:121786200-121788000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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