Variant report

Variant	rs2303001
Chromosome Location	chr5:114566874-114566875
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10045548	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10059069	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10076833	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10079380	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11745083	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs11745170	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs11960213	0.80[EUR][1000 genomes]
rs17640052	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2053697	0.80[EUR][1000 genomes]
rs265417	0.83[ASN][1000 genomes]
rs265437	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs267297	0.82[CEU][hapmap]
rs267298	0.82[CEU][hapmap]
rs3805580	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3805581	0.94[EUR][1000 genomes]
rs3805586	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62383165	0.87[ASN][1000 genomes]
rs62383168	0.80[EUR][1000 genomes]
rs6594883	0.92[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs67276221	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6878733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6884828	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6886102	1.00[CEU][hapmap];0.84[LWK][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7706217	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7725831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9326954	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][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	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
2	nsv1029371	chr5:114541428-114590891	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2303001	PGGT1B	cis	multi-tissue	Pritchard
rs2303001	PGGT1B	cis	normal skin	skin_eQTL
rs2303001	PGGT1B	cis	lymphoblastoid	seeQTL
rs2303001	CCDC112	cis	parietal	SCAN
rs2303001	TRIM36	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114523400-114576200	Weak transcription	Psoas Muscle	Psoas
2	chr5:114530600-114594400	Weak transcription	Pancreas	Pancrea
3	chr5:114538400-114567000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:114538400-114572000	Weak transcription	Lung	lung
5	chr5:114539200-114580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:114540800-114567600	Weak transcription	Hela-S3	cervix
7	chr5:114541800-114573400	Weak transcription	NHLF	lung
8	chr5:114542000-114575800	Weak transcription	Small Intestine	intestine
9	chr5:114543800-114577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:114546800-114575600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:114546800-114578000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:114547600-114577600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:114547800-114578400	Weak transcription	Esophagus	oesophagus
14	chr5:114547800-114596600	Weak transcription	Brain Germinal Matrix	brain
15	chr5:114548400-114596800	Weak transcription	K562	blood
16	chr5:114548800-114575400	Weak transcription	Brain Substantia Nigra	brain
17	chr5:114549400-114597200	Weak transcription	Aorta	Aorta
18	chr5:114549600-114574400	Weak transcription	HMEC	breast
19	chr5:114550200-114568400	Weak transcription	NHEK	skin
20	chr5:114550200-114575400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:114550400-114572600	Weak transcription	A549	lung
22	chr5:114552200-114574600	Weak transcription	Fetal Stomach	stomach
23	chr5:114552200-114581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:114554200-114574600	Weak transcription	Right Ventricle	heart
25	chr5:114554600-114573000	Weak transcription	Brain Angular Gyrus	brain
26	chr5:114554800-114568200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:114555800-114579800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:114556000-114568000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:114556200-114578000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:114556400-114575600	Weak transcription	Fetal Brain Male	brain
31	chr5:114557000-114577400	Weak transcription	Fetal Heart	heart
32	chr5:114557800-114579400	Weak transcription	Gastric	stomach
33	chr5:114558000-114579400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr5:114558800-114568000	Strong transcription	Dnd41	blood
35	chr5:114559000-114587600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr5:114559400-114578200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:114559400-114579400	Weak transcription	Spleen	Spleen
38	chr5:114560200-114568000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:114560600-114567600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:114560600-114577400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr5:114561600-114567600	Strong transcription	Placenta	Placenta
42	chr5:114561600-114568000	Strong transcription	Liver	Liver
43	chr5:114561600-114568600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:114561800-114568000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:114561800-114569000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr5:114561800-114574600	Weak transcription	Fetal Intestine Small	intestine
47	chr5:114562000-114567200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:114562000-114567800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr5:114562000-114567800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr5:114562200-114567800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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