Variant report

Variant	rs2026773
Chromosome Location	chr1:86074975-86074976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86073392..86075755-chr1:86077364..86079429,2	MCF-7	breast:
2	chr1:86045532..86047930-chr1:86071624..86075132,3	MCF-7	breast:
3	chr1:86046246..86048052-chr1:86073407..86075472,2	K562	blood:
4	chr1:86073205..86075088-chr1:86076581..86078830,2	K562	blood:
5	chr1:86041793..86044827-chr1:86073934..86077302,3	K562	blood:
6	chr1:86042110..86043822-chr1:86074708..86077302,2	K562	blood:

Variant related genes	Relation type
ENSG00000153904	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000272691	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12757797	0.80[CHB][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs1999186	0.82[ASN][1000 genomes]
rs2026774	0.81[ASW][hapmap];0.80[CEU][hapmap];0.85[LWK][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4949917	0.86[ASW][hapmap];0.81[YRI][hapmap]
rs4949918	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs6576781	0.82[ASN][1000 genomes]
rs6694808	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs821378	0.81[ASW][hapmap]
rs821390	0.81[ASW][hapmap]
rs821400	0.81[ASW][hapmap]
rs9324152	0.81[ASW][hapmap]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2026773	LOC339524	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86066600-86077000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:86070000-86076800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:86070600-86076600	Weak transcription	Fetal Stomach	stomach
5	chr1:86071200-86076600	Weak transcription	Fetal Lung	lung
6	chr1:86071200-86076800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:86071400-86075000	Enhancers	HSMM	muscle
8	chr1:86071400-86075400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:86071600-86076600	Enhancers	NHDF-Ad	bronchial
10	chr1:86071600-86078800	Enhancers	NHLF	lung
11	chr1:86071800-86076800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:86072200-86077600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:86072400-86076600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:86072400-86076600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:86073000-86078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:86073200-86075200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:86073200-86076800	Weak transcription	Fetal Heart	heart
18	chr1:86073200-86077000	Weak transcription	Ovary	ovary
19	chr1:86073200-86078400	Weak transcription	Pancreas	Pancrea
20	chr1:86073200-86082200	Weak transcription	Aorta	Aorta
21	chr1:86073600-86075400	Weak transcription	Fetal Kidney	kidney
22	chr1:86073600-86076600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:86073600-86076800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:86073600-86078000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:86073800-86076600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:86073800-86077400	Weak transcription	HepG2	liver
27	chr1:86073800-86078400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:86073800-86078600	Weak transcription	Hela-S3	cervix
29	chr1:86074000-86078400	Enhancers	A549	lung
30	chr1:86074200-86075600	Enhancers	Osteobl	bone
31	chr1:86074200-86076400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:86074200-86076400	Weak transcription	NHEK	skin
33	chr1:86074200-86076600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:86074200-86077400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:86074200-86077800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:86074200-86078000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:86074200-86078400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:86074200-86078400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:86074200-86078400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:86074200-86081200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:86074400-86076400	Weak transcription	NH-A	brain
42	chr1:86074400-86076600	Weak transcription	Placenta	Placenta
43	chr1:86074400-86076800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:86074400-86076800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:86074400-86076800	Weak transcription	HMEC	breast
46	chr1:86074400-86077400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:86074400-86077400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:86074400-86077800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:86074400-86077800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:86074400-86078400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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