Variant report

Variant	rs343173
Chromosome Location	chr4:121761018-121761019
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10857073	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857074	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1397767	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1567552	0.94[YRI][hapmap]
rs171067	0.84[AFR][1000 genomes]
rs2102551	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2251270	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2597553	0.86[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2667170	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2667192	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3114953	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs343176	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs343177	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs343183	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs343191	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833673	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6828945	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6846000	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs843557	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs907295	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9991423	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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	nsv879852	chr4:121108734-121768496	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	nsv461634	chr4:121623057-121765527	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv595334	chr4:121623057-121765527	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs343173	PRDM5	cis	Whole Blood	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121729600-121770400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:121743800-121765400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:121750400-121768400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:121751600-121762000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:121753400-121762600	Weak transcription	Osteobl	bone
6	chr4:121755800-121774600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:121756000-121762200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:121756000-121762200	Weak transcription	Fetal Lung	lung
9	chr4:121756600-121763600	Weak transcription	Esophagus	oesophagus
10	chr4:121756800-121779800	Weak transcription	Aorta	Aorta
11	chr4:121758200-121765000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:121758200-121770400	Weak transcription	HSMM	muscle
13	chr4:121758200-121774600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:121758400-121761800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:121758800-121763000	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:121759400-121762800	Weak transcription	NHLF	lung
17	chr4:121759600-121761600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:121759600-121762200	Strong transcription	Fetal Stomach	stomach
19	chr4:121759600-121775400	Weak transcription	Gastric	stomach
20	chr4:121759800-121761400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:121759800-121762000	Strong transcription	Fetal Intestine Small	intestine
22	chr4:121760000-121761200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:121760000-121761200	Genic enhancers	Right Ventricle	heart
24	chr4:121760000-121761200	ZNF genes & repeats	Spleen	Spleen
25	chr4:121760000-121761400	Strong transcription	Fetal Intestine Large	intestine
26	chr4:121760000-121761800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:121760000-121762000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:121760000-121762400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:121760000-121765400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:121760200-121761200	Strong transcription	Fetal Muscle Leg	muscle
31	chr4:121760400-121761400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:121760400-121762000	Enhancers	Fetal Heart	heart
33	chr4:121760400-121775800	Weak transcription	Lung	lung
34	chr4:121760600-121761800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:121760600-121765000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:121760600-121765600	Weak transcription	Ovary	ovary
37	chr4:121760800-121761200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:121760800-121761200	Enhancers	Pancreas	Pancrea
39	chr4:121760800-121761400	Enhancers	Left Ventricle	heart
40	chr4:121760800-121761800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:121761000-121761200	ZNF genes & repeats	Fetal Muscle Trunk	muscle

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