Variant report

Variant	rs41270009
Chromosome Location	chr1:161058927-161058928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161007165..161010190-chr1:161058502..161060475,3	MCF-7	breast:
2	chr1:160989498..160991645-chr1:161056781..161059472,2	MCF-7	breast:
3	chr1:161056990..161060548-chr1:161087703..161089800,3	MCF-7	breast:
4	chr1:161058303..161059850-chr1:161088511..161090425,2	MCF-7	breast:
5	chr1:161014200..161017793-chr1:161057956..161063190,6	MCF-7	breast:
6	chr1:161045029..161046710-chr1:161057509..161060408,2	K562	blood:
7	chr1:161056567..161059211-chr1:161095682..161097348,2	MCF-7	breast:
8	chr1:161043647..161044411-chr1:161058609..161059385,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143256	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000158773	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11265551	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11577230	0.91[EUR][1000 genomes]
rs11590097	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv3351730	chr1:161055728-161059526	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs41270009	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs41270009	TSTD1	cis	Nerve Tibial	GTEx
rs41270009	TSTD1	cis	Artery Tibial	GTEx
rs41270009	TSTD1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161039600-161066800	Weak transcription	Right Atrium	heart
2	chr1:161053200-161059200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:161053600-161063600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:161055200-161064600	Weak transcription	Fetal Lung	lung
5	chr1:161055400-161059200	Active TSS	Esophagus	oesophagus
6	chr1:161055400-161061400	Weak transcription	HSMMtube	muscle
7	chr1:161055400-161062000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:161055400-161062400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:161056800-161059600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:161057000-161062400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:161057200-161059800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:161057600-161059400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:161057600-161059800	Enhancers	HMEC	breast
14	chr1:161057800-161059200	Enhancers	NHDF-Ad	bronchial
15	chr1:161057800-161059600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:161057800-161060000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:161057800-161060200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:161058000-161059000	Enhancers	Osteobl	bone
19	chr1:161058200-161059000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:161058200-161059400	Bivalent/Poised TSS	Fetal Stomach	stomach
21	chr1:161058200-161059400	Flanking Active TSS	NHEK	skin
22	chr1:161058200-161059600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:161058400-161059000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:161058400-161059000	Flanking Active TSS	Pancreas	Pancrea
25	chr1:161058400-161059200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:161058400-161059200	Active TSS	Gastric	stomach
27	chr1:161058400-161059400	Active TSS	Stomach Mucosa	stomach
28	chr1:161058400-161059800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:161058400-161059800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:161058400-161059800	Flanking Active TSS	Placenta	Placenta
31	chr1:161058600-161059000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:161058600-161059000	Active TSS	Lung	lung
33	chr1:161058600-161059000	Active TSS	Placenta Amnion	Placenta Amnion
34	chr1:161058600-161059200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:161058600-161059400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:161058600-161059400	Active TSS	Colonic Mucosa	Colon
37	chr1:161058600-161059400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr1:161058600-161059600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:161058800-161059000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:161058800-161059000	Enhancers	Fetal Intestine Small	intestine
41	chr1:161058800-161059400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:161058800-161059400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr1:161058800-161059400	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr1:161058800-161059400	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:161058800-161059600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr1:161058800-161059800	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:161058800-161060000	Enhancers	Fetal Intestine Large	intestine
48	chr1:161058800-161061400	Weak transcription	HSMM	muscle
49	chr1:161058800-161062000	Weak transcription	NH-A	brain
50	chr1:161058800-161062200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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