Variant report

Variant	rs3805580
Chromosome Location	chr5:114594139-114594140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114592752..114595570-chr5:114596936..114601339,4	K562	blood:
2	chr5:114594074..114596339-chr5:114629566..114632305,2	MCF-7	breast:
3	chr5:114593995..114595570-chr5:114596536..114598747,2	K562	blood:
4	chr5:114594025..114596331-chr5:114597028..114599085,3	MCF-7	breast:
5	chr5:114593990..114598856-chr5:114605325..114609897,4	K562	blood:

Variant related genes	Relation type
ENSG00000271797	Chromatin interaction
ENSG00000164221	Chromatin interaction
ENSG00000164219	Chromatin interaction
ENSG00000243304	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10045548	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10059069	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10076833	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10079380	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11745083	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs11745170	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs17640052	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2303001	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]
rs267297	0.85[CEU][hapmap]
rs267298	0.85[CEU][hapmap]
rs3805581	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3805586	0.90[GIH][hapmap]
rs6594883	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs67276221	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6878733	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6884828	0.81[EUR][1000 genomes]
rs6886102	0.96[CEU][hapmap];0.84[LWK][hapmap];0.90[EUR][1000 genomes]
rs7706217	0.96[CEU][hapmap];0.90[YRI][hapmap];0.95[EUR][1000 genomes]
rs7725831	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9326954	0.96[CEU][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3805580	PGGT1B	cis	multi-tissue	Pritchard
rs3805580	PGGT1B	cis	normal skin	skin_eQTL
rs3805580	CCDC112	cis	parietal	SCAN
rs3805580	PGGT1B	cis	lymphoblastoid	seeQTL
rs3805580	TRIM36	cis	multi-tissue	Pritchard

Chromatin state (count:98 , 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	chr5:114563400-114597600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:114565200-114597400	Weak transcription	Colonic Mucosa	Colon
7	chr5:114575000-114597000	Weak transcription	Fetal Stomach	stomach
8	chr5:114575800-114597000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:114576000-114596800	Weak transcription	Fetal Kidney	kidney
10	chr5:114576000-114596800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:114576200-114596000	Weak transcription	Hela-S3	cervix
12	chr5:114576200-114596800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:114576400-114594400	Weak transcription	Lung	lung
14	chr5:114576600-114596200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:114576600-114596400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:114576600-114597000	Weak transcription	Brain Substantia Nigra	brain
17	chr5:114576800-114596000	Weak transcription	NHDF-Ad	bronchial
18	chr5:114576800-114596400	Weak transcription	Fetal Lung	lung
19	chr5:114576800-114597000	Weak transcription	Thymus	Thymus
20	chr5:114576800-114597400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:114577000-114596800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:114577000-114596800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:114577000-114597200	Weak transcription	Placenta	Placenta
24	chr5:114577200-114595400	Weak transcription	Dnd41	blood
25	chr5:114577200-114596800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:114577400-114596800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:114577600-114594400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:114579600-114596000	Weak transcription	HSMM	muscle
29	chr5:114579600-114596600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:114579600-114597000	Weak transcription	Small Intestine	intestine
31	chr5:114579800-114594200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:114579800-114597000	Weak transcription	Fetal Intestine Small	intestine
33	chr5:114579800-114597400	Weak transcription	Left Ventricle	heart
34	chr5:114582600-114594200	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:114584600-114594800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr5:114584600-114596800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:114584600-114597000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:114584600-114597000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:114584600-114597000	Weak transcription	Fetal Intestine Large	intestine
40	chr5:114584600-114597000	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:114584600-114597200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:114585400-114596000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:114585400-114597000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr5:114585400-114597200	Weak transcription	Fetal Thymus	thymus
45	chr5:114586600-114594400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:114587400-114596000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:114587800-114594400	Weak transcription	A549	lung
48	chr5:114587800-114596000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:114587800-114597000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:114588600-114595800	Weak transcription	NHEK	skin

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