Variant report

Variant	rs1084525
Chromosome Location	chr2:55929430-55929431
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55923895..55927237-chr2:55928589..55931342,3	K562	blood:
2	chr2:55924095..55926502-chr2:55928603..55930302,2	K562	blood:
3	chr2:55843167..55845991-chr2:55928985..55931317,2	MCF-7	breast:
4	chr2:55929391..55931366-chr2:55933067..55934702,2	K562	blood:

Variant related genes	Relation type
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10460508	0.85[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs10496050	0.83[ASW][hapmap];0.82[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs1084522	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12329050	0.90[YRI][hapmap]
rs12616629	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17278044	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17369191	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs1823893	0.82[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1975484	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs1975487	0.81[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs2586950	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2586952	0.81[ASN][1000 genomes]
rs2586954	0.85[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2586969	1.00[YRI][hapmap]
rs2586970	1.00[YRI][hapmap]
rs2627765	0.84[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs2627767	0.81[AMR][1000 genomes]
rs2627769	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627772	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2627773	0.93[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2627775	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap]
rs2627776	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2627779	0.82[AFR][1000 genomes]
rs2868428	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35504023	0.83[ASW][hapmap];0.82[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs4290693	0.83[ASW][hapmap];0.82[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs4312532	0.95[YRI][hapmap]
rs62165255	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6545506	0.82[ASW][hapmap];0.81[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs706548	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7582278	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7596377	0.91[YRI][hapmap]
rs782566	0.80[AMR][1000 genomes]
rs782567	0.80[AMR][1000 genomes]
rs782568	0.85[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs782572	0.96[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs782573	0.96[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs782584	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782585	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782586	0.83[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs782588	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs782590	0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs782595	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs782599	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs782602	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs782606	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs782607	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs782619	0.85[AMR][1000 genomes]
rs782622	0.85[AMR][1000 genomes]
rs782629	0.83[ASW][hapmap];0.93[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs782630	0.92[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs782632	0.93[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs782633	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs782634	0.82[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs782637	0.83[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs782641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782642	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782644	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs782652	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap]
rs809732	0.96[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs935177	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv2762645	chr2:55892248-55963418	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv2760573	chr2:55903016-55941440	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv9802	chr2:55910254-55939253	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv16137	chr2:55910848-55938746	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv442740	chr2:55914790-55938579	Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv514069	chr2:55914952-55938116	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1084525	PNPT1	cis	cerebellum	SCAN
rs1084525	PNPT1	cis	lymphoblastoid	seeQTL
rs1084525	POMC	trans	lymphoblastoid	seeQTL
rs1084525	SMEK2	cis	parietal	SCAN
rs1084525	PNPT1	Cis_1M	lymphoblastoid	RTeQTL
rs1084525	CCDC104	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55927000-55934600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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