Variant report

Variant	rs6674131
Chromosome Location	chr1:56991294-56991295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1041602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416285	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs17470169	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1759753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1819750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3927760	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3927761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41487448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772578	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs61772592	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772593	1.00[AFR][1000 genomes]
rs61772595	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772618	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772620	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772622	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772623	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772625	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772626	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772627	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688009	0.89[CEU][hapmap]
rs857131	1.00[CHB][hapmap]
rs9437006	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6674131	PCSK9	cis	cerebellum	SCAN
rs6674131	RAB31	trans	lymphoblastoid	seeQTL
rs6674131	LRP8	cis	cerebellum	SCAN
rs6674131	DIO1	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:56976400-56991600	Strong transcription	Fetal Stomach	stomach
3	chr1:56976800-56992400	Weak transcription	Brain Germinal Matrix	brain
4	chr1:56977800-56999200	Weak transcription	A549	lung
5	chr1:56978000-56991400	Weak transcription	Fetal Brain Male	brain
6	chr1:56978000-56992600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:56979200-56992600	Strong transcription	HepG2	liver
8	chr1:56980600-56991600	Genic enhancers	Left Ventricle	heart
9	chr1:56983200-56991400	Strong transcription	Osteobl	bone
10	chr1:56983200-56992400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:56983400-56992200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:56983400-57000800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:56984200-56992000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:56984200-56992200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:56984200-56992400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:56985000-56993400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:56985000-56993600	Weak transcription	Fetal Brain Female	brain
18	chr1:56985400-56991400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr1:56986000-56991600	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:56986200-56992600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:56986800-56992000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:56987000-56991400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:56987000-56991800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
25	chr1:56987600-56994200	Enhancers	Dnd41	blood
26	chr1:56987800-56993000	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:56988400-56991600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:56988400-56992800	Enhancers	Right Atrium	heart
29	chr1:56988400-56993800	Enhancers	Primary B cells from peripheral blood	blood
30	chr1:56988800-56991800	Weak transcription	Stomach Mucosa	stomach
31	chr1:56988800-56992000	Weak transcription	Fetal Heart	heart
32	chr1:56988800-56992200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:56989000-56991400	Strong transcription	Aorta	Aorta
34	chr1:56989400-56991400	Enhancers	GM12878-XiMat	blood
35	chr1:56989400-56993600	Enhancers	Primary B cells from cord blood	blood
36	chr1:56989600-56992400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:56989800-56992400	Weak transcription	NH-A	brain
38	chr1:56990000-56992600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:56990000-56995200	Genic enhancers	Fetal Muscle Leg	muscle
40	chr1:56990000-57004000	Genic enhancers	Liver	Liver
41	chr1:56990200-56991400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:56990200-56991400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:56990200-56991600	Weak transcription	Colonic Mucosa	Colon
44	chr1:56990200-56991800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:56990200-56992000	Enhancers	Spleen	Spleen
46	chr1:56990200-56992400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:56990200-56992400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:56990200-56992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:56990200-56992800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:56990200-56993600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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