Variant report

Variant	rs2974528
Chromosome Location	chr5:114462630-114462631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13160731	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1422068	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1422070	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[EUR][1000 genomes]
rs1990896	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2121187	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs265403	0.82[CHB][hapmap]
rs2974618	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2974619	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3936303	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4705729	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56805857	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60548555	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62381516	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6594876	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6594877	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6594878	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6859313	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6866580	0.95[CHB][hapmap];0.83[GIH][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7704583	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7708481	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7732228	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9654507	0.86[AMR][1000 genomes];0.83[EUR][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	nsv882729	chr5:113743628-114497708	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv830453	chr5:114277261-114546536	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv462398	chr5:114445023-114475774	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv599476	chr5:114445023-114475774	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv462399	chr5:114445023-114526010	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv599477	chr5:114445023-114526010	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2974528	PGGT1B	cis	uninvolved skin	skin_eQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114453800-114500600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:114458800-114465800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:114460000-114476000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:114460400-114465800	Weak transcription	Brain Germinal Matrix	brain
5	chr5:114460400-114470800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:114460400-114486800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:114460600-114462800	Weak transcription	Fetal Brain Female	brain
8	chr5:114460600-114464600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:114460600-114466000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:114460600-114468000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:114460800-114489200	Weak transcription	Aorta	Aorta
12	chr5:114461000-114489200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:114461800-114464600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:114461800-114467400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:114462000-114465000	Strong transcription	Duodenum Mucosa	Duodenum
16	chr5:114462000-114472400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:114462200-114464000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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