Variant report

Variant	rs956157
Chromosome Location	chr2:56673449-56673450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10174257	0.96[EUR][1000 genomes]
rs10184667	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1030333	0.92[EUR][1000 genomes]
rs1030334	0.92[EUR][1000 genomes]
rs11125631	0.95[EUR][1000 genomes]
rs1157475	0.95[EUR][1000 genomes]
rs11688894	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11885335	0.93[EUR][1000 genomes]
rs11903884	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13396394	0.90[EUR][1000 genomes]
rs13397156	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1465359	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1465360	0.89[EUR][1000 genomes]
rs1465362	0.92[EUR][1000 genomes]
rs1465363	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17047946	0.96[EUR][1000 genomes]
rs17047952	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17047955	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17047986	0.81[EUR][1000 genomes]
rs2033015	0.90[EUR][1000 genomes]
rs2160707	0.98[EUR][1000 genomes]
rs2193486	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2193487	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2869810	0.82[EUR][1000 genomes]
rs2869827	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2869828	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4614971	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6753780	0.89[EUR][1000 genomes]
rs72618681	0.81[EUR][1000 genomes]
rs7587750	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7598538	0.98[EUR][1000 genomes]
rs986787	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs986788	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834093	chr2:56538097-56708677	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1004449	chr2:56538460-56715861	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv874171	chr2:56545845-56727178	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv522944	chr2:56603985-56676997	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv874172	chr2:56638856-56811749	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2757800	chr2:56659685-56851198	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2759052	chr2:56659685-56851198	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs956157	PNPT1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56672000-56675000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:56672000-56675200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:56672000-56675600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:56672000-56675800	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:56672200-56675200	Weak transcription	Psoas Muscle	Psoas
6	chr2:56672200-56675400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:56672200-56675600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:56672200-56675600	Weak transcription	Stomach Mucosa	stomach
9	chr2:56672200-56675800	Weak transcription	Gastric	stomach
10	chr2:56673000-56674400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:56673200-56674400	Weak transcription	Fetal Intestine Large	intestine

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