Variant report

Variant	rs1319274
Chromosome Location	chr1:56974091-56974092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56973352..56978913-chr1:56979369..56985140,11	K562	blood:

Variant related genes	Relation type
ENSG00000162407	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1261412	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1261413	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1261414	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1361823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17114046	1.00[CHD][hapmap]
rs17407790	1.00[CHB][hapmap]
rs1777276	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2798153	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56198059	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61772594	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9970807	1.00[CHD][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1319274	PCSK9	cis	cerebellum	SCAN
rs1319274	DIO1	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56957800-56975600	Weak transcription	Fetal Brain Female	brain
2	chr1:56958000-56975600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:56958000-56977000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:56960800-56976000	Genic enhancers	HepG2	liver
5	chr1:56962400-56976000	Weak transcription	NH-A	brain
6	chr1:56964800-56976000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:56964800-56979200	Genic enhancers	NHDF-Ad	bronchial
8	chr1:56965000-56975600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:56965200-56975600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr1:56965200-56975600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:56965800-56975600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:56965800-56975800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:56966000-56980600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:56966800-56974600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:56966800-56975800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:56967400-56978400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:56967800-56975600	Weak transcription	Fetal Brain Male	brain
19	chr1:56968000-56976000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:56968200-56975000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:56968200-56975400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:56968600-56975600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:56968800-56974400	Strong transcription	A549	lung
24	chr1:56969000-56979200	Genic enhancers	Lung	lung
25	chr1:56970200-56974800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:56970400-56977400	Genic enhancers	Fetal Intestine Large	intestine
27	chr1:56970800-56975000	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr1:56970800-56975200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:56970800-56977400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:56970800-56978000	Genic enhancers	Fetal Intestine Small	intestine
31	chr1:56970800-56978200	Enhancers	Right Atrium	heart
32	chr1:56971000-56978000	Strong transcription	Thymus	Thymus
33	chr1:56971000-56979200	Genic enhancers	Left Ventricle	heart
34	chr1:56971400-56977000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:56971400-56986200	Genic enhancers	Placenta	Placenta
36	chr1:56971600-56974600	Genic enhancers	Ovary	ovary
37	chr1:56971600-56974800	Genic enhancers	Esophagus	oesophagus
38	chr1:56971600-56975000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:56971600-56975200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:56971600-56976400	Enhancers	Psoas Muscle	Psoas
41	chr1:56971600-56977200	Genic enhancers	Fetal Thymus	thymus
42	chr1:56971600-56977800	Genic enhancers	Fetal Muscle Leg	muscle
43	chr1:56971600-56978200	Genic enhancers	Right Ventricle	heart
44	chr1:56971600-56978400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:56971600-56979200	Genic enhancers	Adipose Nuclei	Adipose
46	chr1:56971800-56974400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr1:56971800-56974800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:56971800-56974800	Enhancers	HMEC	breast
49	chr1:56971800-56975000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:56971800-56975000	Enhancers	NHEK	skin

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