Variant report

Variant	rs343176
Chromosome Location	chr4:121759338-121759339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10857073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857074	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1397767	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567552	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs171067	0.93[AFR][1000 genomes]
rs2102551	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251270	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2597553	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]
rs2667170	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667192	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3114953	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs343173	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];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs343183	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833673	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6828945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6846000	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs843557	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs907295	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9991423	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs343176	PRDM5	cis	Whole Blood	GTEx
rs343176	SYNPO2	cis	parietal	SCAN
rs343176	QRFPR	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121729600-121770400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:121730400-121760000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:121730400-121760800	Weak transcription	Pancreas	Pancrea
4	chr4:121737600-121759800	Weak transcription	Lung	lung
5	chr4:121738200-121759600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:121743800-121765400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:121750400-121768400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:121751600-121762000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:121751800-121759600	Weak transcription	Ovary	ovary
10	chr4:121753400-121762600	Weak transcription	Osteobl	bone
11	chr4:121754600-121760000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:121755600-121759600	Weak transcription	Fetal Stomach	stomach
13	chr4:121755800-121760000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:121755800-121774600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:121756000-121760000	Weak transcription	Fetal Intestine Large	intestine
16	chr4:121756000-121762200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:121756000-121762200	Weak transcription	Fetal Lung	lung
18	chr4:121756200-121759800	Weak transcription	Fetal Intestine Small	intestine
19	chr4:121756600-121763600	Weak transcription	Esophagus	oesophagus
20	chr4:121756800-121759600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:121756800-121760400	Weak transcription	Fetal Heart	heart
22	chr4:121756800-121779800	Weak transcription	Aorta	Aorta
23	chr4:121757000-121759800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:121757200-121760200	Weak transcription	Fetal Muscle Leg	muscle
25	chr4:121757200-121760800	Weak transcription	Left Ventricle	heart
26	chr4:121758000-121759800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:121758200-121765000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:121758200-121770400	Weak transcription	HSMM	muscle
29	chr4:121758200-121774600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:121758400-121761800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:121758600-121760800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:121758800-121763000	Weak transcription	Colon Smooth Muscle	Colon
33	chr4:121759200-121760000	Weak transcription	Right Ventricle	heart

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