Variant report

Variant	rs10077453
Chromosome Location	chr5:114580652-114580653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10059320	0.91[JPT][hapmap];0.96[MKK][hapmap]
rs1017208	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11950355	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13152930	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13172537	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17459144	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2305130	1.00[JPT][hapmap];0.92[MKK][hapmap]
rs267304	0.85[MKK][hapmap]
rs28379874	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2909842	0.85[ASN][1000 genomes]
rs2909843	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2925185	0.89[ASN][1000 genomes]
rs2963769	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2963770	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2963771	0.90[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2963772	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2963773	1.00[JPT][hapmap]
rs2963774	0.85[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2964543	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2964544	0.85[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34434304	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35948019	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4041	1.00[JPT][hapmap];0.96[MKK][hapmap]
rs4705732	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7734074	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9326953	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9326956	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.85[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10077453	CCDC112	cis	parietal	SCAN
rs10077453	PGGT1B	cis	uninvolved skin	skin_eQTL
rs10077453	PGGT1B	cis	brain	BrainEAC
rs10077453	EMR2	trans	lymphoblastoid	seeQTL
rs10077453	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs10077453	PGGT1B	cis	lymphoblastoid	seeQTL
rs10077453	STARD4	cis	parietal	SCAN
rs10077453	PGGT1B	cis	lesional skin	skin_eQTL
rs10077453	PGGT1B	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114530600-114594400	Weak transcription	Pancreas	Pancrea
2	chr5:114547800-114596600	Weak transcription	Brain Germinal Matrix	brain
3	chr5:114548400-114596800	Weak transcription	K562	blood
4	chr5:114549400-114597200	Weak transcription	Aorta	Aorta
5	chr5:114552200-114581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:114559000-114587600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:114563400-114591600	Weak transcription	Brain Anterior Caudate	brain
8	chr5:114563400-114597600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:114565200-114597400	Weak transcription	Colonic Mucosa	Colon
10	chr5:114567400-114590600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:114567800-114589800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:114573400-114586000	Weak transcription	A549	lung
13	chr5:114573800-114586000	Weak transcription	Brain Angular Gyrus	brain
14	chr5:114575000-114597000	Weak transcription	Fetal Stomach	stomach
15	chr5:114575800-114597000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:114576000-114596800	Weak transcription	Fetal Kidney	kidney
17	chr5:114576000-114596800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:114576200-114591000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr5:114576200-114596000	Weak transcription	Hela-S3	cervix
20	chr5:114576200-114596800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:114576400-114584000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr5:114576400-114590600	Weak transcription	Ovary	ovary
23	chr5:114576400-114594400	Weak transcription	Lung	lung
24	chr5:114576600-114582400	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:114576600-114585000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:114576600-114586400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:114576600-114590800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:114576600-114593000	Weak transcription	HSMMtube	muscle
29	chr5:114576600-114596200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:114576600-114596400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:114576600-114597000	Weak transcription	Brain Substantia Nigra	brain
32	chr5:114576800-114585000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:114576800-114585000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:114576800-114591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:114576800-114596000	Weak transcription	NHDF-Ad	bronchial
36	chr5:114576800-114596400	Weak transcription	Fetal Lung	lung
37	chr5:114576800-114597000	Weak transcription	Thymus	Thymus
38	chr5:114576800-114597400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr5:114577000-114584200	Weak transcription	Fetal Muscle Leg	muscle
40	chr5:114577000-114590800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:114577000-114591600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:114577000-114591800	Weak transcription	Psoas Muscle	Psoas
43	chr5:114577000-114596800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr5:114577000-114596800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:114577000-114597200	Weak transcription	Placenta	Placenta
46	chr5:114577200-114595400	Weak transcription	Dnd41	blood
47	chr5:114577200-114596800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:114577400-114583800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:114577400-114584200	Weak transcription	Fetal Intestine Large	intestine
50	chr5:114577400-114585000	Weak transcription	Primary T cells fromperipheralblood	blood

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