Variant report

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10055468	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057172	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059320	0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061960	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070542	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077453	1.00[JPT][hapmap]
rs1017208	1.00[JPT][hapmap]
rs11950355	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17459144	0.86[JPT][hapmap]
rs2305130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909843	1.00[JPT][hapmap]
rs2963769	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2963770	0.86[JPT][hapmap]
rs2963771	1.00[JPT][hapmap]
rs2963773	1.00[JPT][hapmap]
rs2963774	0.86[JPT][hapmap]
rs2964543	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2964544	1.00[JPT][hapmap]
rs4041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596375	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705732	1.00[JPT][hapmap]
rs7734074	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9326953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10078804	PGGT1B	cis	multi-tissue	Pritchard
rs10078804	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114522800-114543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:114523000-114526800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:114523400-114576200	Weak transcription	Psoas Muscle	Psoas
4	chr5:114525200-114526600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:114525400-114526200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:114525400-114526400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:114525400-114526400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr5:114525400-114526400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:114525400-114526400	Enhancers	Gastric	stomach
10	chr5:114525400-114526600	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr5:114525400-114527400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr5:114525400-114531400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr5:114525600-114526200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr5:114525600-114526200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:114525600-114526400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr5:114525600-114526600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:114525600-114528200	Enhancers	Stomach Mucosa	stomach
18	chr5:114525800-114526600	Weak transcription	Colonic Mucosa	Colon
19	chr5:114525800-114544800	Weak transcription	Primary T cells from cord blood	blood
20	chr5:114526000-114528600	Enhancers	Duodenum Mucosa	Duodenum

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