Variant report

Variant	rs1930762
Chromosome Location	chr1:56997782-56997783
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	chr1:56996284..56998415-chr1:56998780..57000786,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10888977	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11206833	0.89[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12082242	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1261411	0.82[ASW][hapmap]
rs1759750	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1759752	0.88[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1777274	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1777277	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1810930	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1930760	0.93[YRI][hapmap]
rs4532850	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4628	0.89[CEU][hapmap]
rs4912314	0.81[JPT][hapmap]
rs4912377	0.84[CEU][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55798508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515808	0.81[JPT][hapmap]
rs7529520	0.83[YRI][hapmap];0.88[EUR][1000 genomes]
rs7535757	0.94[ASW][hapmap];0.85[CEU][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7556056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953856	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs993075	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1930762	PCSK9	cis	cerebellum	SCAN
rs1930762	ACOT11	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

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	chr1:56977800-56999200	Weak transcription	A549	lung
3	chr1:56983400-57000800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
5	chr1:56990000-57004000	Genic enhancers	Liver	Liver
6	chr1:56990200-56998600	Enhancers	Brain Substantia Nigra	brain
7	chr1:56990600-56997800	Enhancers	Brain Anterior Caudate	brain
8	chr1:56992000-57001200	Weak transcription	Spleen	Spleen
9	chr1:56992800-56997800	Weak transcription	HSMMtube	muscle
10	chr1:56992800-56998600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:56992800-56998800	Weak transcription	Gastric	stomach
12	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
13	chr1:56993000-56998800	Enhancers	Ovary	ovary
14	chr1:56993000-56999800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:56993000-57004600	Weak transcription	Hela-S3	cervix
16	chr1:56993200-57001400	Enhancers	Right Atrium	heart
17	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
18	chr1:56993800-56998000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:56993800-56998200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:56993800-57004200	Weak transcription	NH-A	brain
21	chr1:56994000-56997800	Weak transcription	Esophagus	oesophagus
22	chr1:56994000-56997800	Weak transcription	Thymus	Thymus
23	chr1:56994000-56998600	Weak transcription	Colonic Mucosa	Colon
24	chr1:56994000-56999000	Weak transcription	Aorta	Aorta
25	chr1:56994000-57000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:56994000-57001200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:56994000-57004000	Weak transcription	HUVEC	blood vessel
28	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
29	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
30	chr1:56994200-56998000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:56994200-56998800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:56994200-56999400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:56994200-57001200	Weak transcription	Dnd41	blood
34	chr1:56994200-57004400	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr1:56994400-56998400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:56994400-57002600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:56994600-56998400	Enhancers	Psoas Muscle	Psoas
38	chr1:56994600-56999600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:56994600-56999800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:56994800-56998000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:56994800-56999000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
42	chr1:56995000-56998000	Enhancers	Left Ventricle	heart
43	chr1:56995000-56998200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:56995000-56998200	Strong transcription	Fetal Stomach	stomach
45	chr1:56995000-56998400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr1:56995000-57003400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:56995000-57003600	Strong transcription	Osteobl	bone
48	chr1:56995200-56999800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:56995200-57000000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:56995200-57003800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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