Variant report

Variant	rs267304
Chromosome Location	chr5:114589908-114589909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114588379..114591127-chr5:114596921..114598565,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271797	Chromatin interaction
ENSG00000164219	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10059320	0.81[MKK][hapmap]
rs10077453	0.85[MKK][hapmap]
rs117060	0.92[CHB][hapmap]
rs155414	0.86[CEU][hapmap];0.91[CHB][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs155573	0.87[CEU][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs169088	0.87[CEU][hapmap];0.92[CHB][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs185566	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs190561	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053697	0.85[CHB][hapmap];0.93[CHD][hapmap]
rs2305130	0.85[MKK][hapmap]
rs265412	0.89[CHD][hapmap]
rs265418	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs265419	0.92[CHB][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs265420	0.91[CEU][hapmap];0.92[CHB][hapmap];0.91[EUR][1000 genomes]
rs265421	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs265424	0.96[EUR][1000 genomes]
rs265425	1.00[ASW][hapmap];0.87[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs265430	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs265435	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs265436	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs265438	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs265439	0.87[CEU][hapmap];0.92[CHB][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs265442	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs267286	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs267287	0.83[CHB][hapmap]
rs267288	0.83[CHB][hapmap]
rs267295	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs267297	0.93[CHD][hapmap]
rs267298	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs267299	0.92[CHB][hapmap]
rs267300	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs267301	0.92[CHB][hapmap]
rs267302	1.00[CHB][hapmap]
rs267303	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs267306	0.83[ASN][1000 genomes]
rs267307	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[ASN][1000 genomes]
rs3100784	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs3111172	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4041	0.81[MKK][hapmap]
rs9326953	0.85[MKK][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs267304	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs267304	PGGT1B	cis	uninvolved skin	skin_eQTL
rs267304	PGGT1B	cis	lesional skin	skin_eQTL
rs267304	PGGT1B	cis	lymphoblastoid	seeQTL
rs267304	PGGT1B	cis	multi-tissue	Pritchard
rs267304	PGGT1B	cis	normal skin	skin_eQTL
rs267304	CCDC112	cis	parietal	SCAN

Chromatin state (count:93 , 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	chr5:114563400-114591600	Weak transcription	Brain Anterior Caudate	brain
6	chr5:114563400-114597600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:114565200-114597400	Weak transcription	Colonic Mucosa	Colon
8	chr5:114567400-114590600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:114575000-114597000	Weak transcription	Fetal Stomach	stomach
10	chr5:114575800-114597000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:114576000-114596800	Weak transcription	Fetal Kidney	kidney
12	chr5:114576000-114596800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:114576200-114591000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr5:114576200-114596000	Weak transcription	Hela-S3	cervix
15	chr5:114576200-114596800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:114576400-114590600	Weak transcription	Ovary	ovary
17	chr5:114576400-114594400	Weak transcription	Lung	lung
18	chr5:114576600-114590800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:114576600-114593000	Weak transcription	HSMMtube	muscle
20	chr5:114576600-114596200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:114576600-114596400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:114576600-114597000	Weak transcription	Brain Substantia Nigra	brain
23	chr5:114576800-114591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:114576800-114596000	Weak transcription	NHDF-Ad	bronchial
25	chr5:114576800-114596400	Weak transcription	Fetal Lung	lung
26	chr5:114576800-114597000	Weak transcription	Thymus	Thymus
27	chr5:114576800-114597400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:114577000-114590800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:114577000-114591600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr5:114577000-114591800	Weak transcription	Psoas Muscle	Psoas
31	chr5:114577000-114596800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:114577000-114596800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:114577000-114597200	Weak transcription	Placenta	Placenta
34	chr5:114577200-114595400	Weak transcription	Dnd41	blood
35	chr5:114577200-114596800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:114577400-114591400	Weak transcription	Adipose Nuclei	Adipose
37	chr5:114577400-114596800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:114577600-114591600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:114577600-114594400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:114577800-114594000	Weak transcription	Primary T cells from cord blood	blood
41	chr5:114579600-114593200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:114579600-114593400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:114579600-114593400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:114579600-114594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:114579600-114594000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:114579600-114596000	Weak transcription	HSMM	muscle
47	chr5:114579600-114596600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:114579600-114597000	Weak transcription	Small Intestine	intestine
49	chr5:114579800-114590400	Weak transcription	Liver	Liver
50	chr5:114579800-114591800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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