Variant report

Variant	rs2061054
Chromosome Location	chr8:98994851-98994852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:98985735..98990217-chr8:98991050..98995817,5	K562	blood:
2	chr8:98994617..98996981-chr8:99019389..99021453,2	MCF-7	breast:
3	chr8:98992573..98995424-chr8:98996000..98998679,2	MCF-7	breast:
4	chr8:98786769..98788995-chr8:98993109..98995354,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104341	Chromatin interaction
ENSG00000132561	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1869609	0.81[JPT][hapmap]
rs2085144	1.00[LWK][hapmap]
rs2512040	0.84[CHB][hapmap]
rs2512046	0.81[JPT][hapmap]
rs2513806	1.00[CEU][hapmap]
rs964141	1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv528695	chr8:98960813-99022009	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2061054	SEC1	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98976200-98996200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:98985600-98995800	Weak transcription	A549	lung
3	chr8:98986000-98997400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr8:98987400-98998400	Weak transcription	Pancreas	Pancrea
5	chr8:98988000-99011800	Weak transcription	Aorta	Aorta
6	chr8:98989200-98997200	Weak transcription	Liver	Liver
7	chr8:98990600-98997200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr8:98990800-98997000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr8:98991000-98997800	Enhancers	Osteobl	bone
10	chr8:98992200-98996400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr8:98992200-98998200	Enhancers	NHLF	lung
12	chr8:98992600-98995800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr8:98992600-98996000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr8:98992600-98996000	Weak transcription	HMEC	breast
15	chr8:98992600-99019400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr8:98992800-98996400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr8:98992800-98996600	Weak transcription	NHEK	skin
18	chr8:98993400-98995800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:98994000-98995200	Enhancers	Fetal Stomach	stomach
20	chr8:98994000-98995600	Weak transcription	HSMMtube	muscle
21	chr8:98994000-98995800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:98994200-98995200	Weak transcription	NHDF-Ad	bronchial
23	chr8:98994200-98995600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr8:98994200-98996200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr8:98994200-99014800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr8:98994400-98995600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr8:98994400-98995600	Weak transcription	HSMM	muscle
28	chr8:98994400-98995600	Weak transcription	NH-A	brain
29	chr8:98994400-98995800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr8:98994400-98997200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr8:98994400-99003200	Weak transcription	Brain Substantia Nigra	brain
32	chr8:98994600-98996000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr8:98994600-98996400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr8:98994600-98997400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr8:98994600-98997400	Weak transcription	Brain Hippocampus Middle	brain
36	chr8:98994600-98998000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr8:98994600-99008200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr8:98994600-99008400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr8:98994600-99014200	Weak transcription	Ovary	ovary
40	chr8:98994800-98995200	Weak transcription	Fetal Muscle Leg	muscle

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