Variant report

Variant	rs10874427
Chromosome Location	chr1:84533132-84533133
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84530745..84533538-chr1:84541261..84543799,3	K562	blood:
2	chr1:84525894..84527456-chr1:84531489..84533439,2	K562	blood:

Variant related genes	Relation type
ENSG00000142875	Chromatin interaction
ENSG00000271576	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1021491	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1057738	0.87[JPT][hapmap]
rs10874428	0.87[JPT][hapmap]
rs10874432	0.85[JPT][hapmap]
rs11163897	0.83[AMR][1000 genomes]
rs11163903	0.87[JPT][hapmap]
rs11163905	0.87[JPT][hapmap]
rs11163906	0.87[JPT][hapmap]
rs11163907	0.87[JPT][hapmap]
rs11163908	0.87[JPT][hapmap]
rs11163911	0.87[JPT][hapmap]
rs11163913	0.87[JPT][hapmap]
rs12057561	0.86[JPT][hapmap]
rs12118723	0.87[JPT][hapmap]
rs12132002	0.82[JPT][hapmap]
rs12565896	0.87[JPT][hapmap]
rs12723299	0.87[JPT][hapmap]
rs12748859	0.87[JPT][hapmap]
rs12750691	0.87[JPT][hapmap]
rs1402694	0.87[JPT][hapmap]
rs1472243	0.87[JPT][hapmap]
rs1521518	0.90[JPT][hapmap]
rs1603000	1.00[CEU][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs1874070	0.87[JPT][hapmap]
rs2037454	0.87[JPT][hapmap]
rs2134648	0.87[JPT][hapmap]
rs2134649	0.87[JPT][hapmap]
rs2250806	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2642186	1.00[CEU][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs2792973	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2792975	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2792976	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907194	0.85[JPT][hapmap]
rs594631	0.83[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs599686	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603939	1.00[CEU][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs617568	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs638545	0.87[EUR][1000 genomes]
rs648856	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650629	0.87[EUR][1000 genomes]
rs652489	0.84[EUR][1000 genomes]
rs6576959	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6576960	0.86[JPT][hapmap]
rs6576961	0.86[JPT][hapmap]
rs6576962	0.87[JPT][hapmap]
rs6576963	0.87[JPT][hapmap]
rs6674038	0.83[AMR][1000 genomes]
rs6695305	0.87[JPT][hapmap]
rs6695851	0.87[JPT][hapmap]
rs6696125	0.87[JPT][hapmap]
rs6701486	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6703653	0.84[MEX][hapmap]
rs7515976	0.87[JPT][hapmap]
rs7520283	0.84[MEX][hapmap]
rs7547892	0.87[JPT][hapmap]
rs903263	0.87[JPT][hapmap]
rs957828	0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1732	chr1:84499098-84544635	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv871655	chr1:84517261-84550849	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3379138	chr1:84531980-84545128	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10874427	PRKACB	cis	lymphoblastoid	seeQTL
rs10874427	MCOLN2	cis	parietal	SCAN
rs10874427	LOC339524	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84532600-84533600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:84532800-84533600	Enhancers	Brain Hippocampus Middle	brain
3	chr1:84533000-84533400	Enhancers	Brain Inferior Temporal Lobe	brain

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