Variant report

Variant	rs265442
Chromosome Location	chr5:114571758-114571759
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114533126..114535353-chr5:114570150..114573144,2	K562	blood:
2	chr5:114504037..114507860-chr5:114568849..114572431,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152503	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs117060	0.84[CHB][hapmap]
rs155414	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs155573	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169088	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs185566	0.92[CHD][hapmap]
rs190561	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2053697	0.92[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs265412	0.89[CHD][hapmap]
rs265418	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs265419	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs265420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs265421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs265424	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs265425	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs265430	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs265435	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs265436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs265437	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs265438	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs265439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267286	0.92[CHD][hapmap]
rs267295	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs267297	0.93[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs267298	0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs267299	0.84[CHB][hapmap]
rs267300	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs267301	0.84[CHB][hapmap]
rs267302	0.92[CHB][hapmap]
rs267303	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs267304	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]
rs267307	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs3100784	0.84[CHB][hapmap];0.96[CHD][hapmap]
rs3111172	0.91[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs265442	PGGT1B	cis	uninvolved skin	skin_eQTL
rs265442	PGGT1B	cis	lymphoblastoid	seeQTL
rs265442	PGGT1B	cis	normal skin	skin_eQTL
rs265442	PGGT1B	cis	multi-tissue	Pritchard
rs265442	CCDC112	cis	parietal	SCAN
rs265442	PGGT1B	cis	lesional skin	skin_eQTL
rs265442	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs265442	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	chr5:114538400-114572000	Weak transcription	Lung	lung
4	chr5:114539200-114580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:114541800-114573400	Weak transcription	NHLF	lung
6	chr5:114542000-114575800	Weak transcription	Small Intestine	intestine
7	chr5:114543800-114577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:114546800-114575600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:114546800-114578000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr5:114547600-114577600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:114547800-114578400	Weak transcription	Esophagus	oesophagus
12	chr5:114547800-114596600	Weak transcription	Brain Germinal Matrix	brain
13	chr5:114548400-114596800	Weak transcription	K562	blood
14	chr5:114548800-114575400	Weak transcription	Brain Substantia Nigra	brain
15	chr5:114549400-114597200	Weak transcription	Aorta	Aorta
16	chr5:114549600-114574400	Weak transcription	HMEC	breast
17	chr5:114550200-114575400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:114550400-114572600	Weak transcription	A549	lung
19	chr5:114552200-114574600	Weak transcription	Fetal Stomach	stomach
20	chr5:114552200-114581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:114554200-114574600	Weak transcription	Right Ventricle	heart
22	chr5:114554600-114573000	Weak transcription	Brain Angular Gyrus	brain
23	chr5:114555800-114579800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr5:114556200-114578000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:114556400-114575600	Weak transcription	Fetal Brain Male	brain
26	chr5:114557000-114577400	Weak transcription	Fetal Heart	heart
27	chr5:114557800-114579400	Weak transcription	Gastric	stomach
28	chr5:114558000-114579400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:114559000-114587600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr5:114559400-114578200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:114559400-114579400	Weak transcription	Spleen	Spleen
32	chr5:114560600-114577400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr5:114561800-114574600	Weak transcription	Fetal Intestine Small	intestine
34	chr5:114562400-114577600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:114562400-114577600	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:114563200-114578400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:114563400-114574600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:114563400-114574600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:114563400-114575400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr5:114563400-114578600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:114563400-114591600	Weak transcription	Brain Anterior Caudate	brain
42	chr5:114563400-114597600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:114565000-114575000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:114565000-114575600	Weak transcription	HSMMtube	muscle
45	chr5:114565200-114597400	Weak transcription	Colonic Mucosa	Colon
46	chr5:114565600-114574600	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:114565600-114574600	Weak transcription	Colon Smooth Muscle	Colon
48	chr5:114565800-114575400	Weak transcription	Fetal Brain Female	brain
49	chr5:114566000-114572000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:114566000-114574000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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