Variant report

Variant	rs2840591
Chromosome Location	chr1:159940000-159940001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:159905137..159907886-chr1:159939775..159941971,2	MCF-7	breast:
2	chr1:159914982..159917172-chr1:159939218..159941939,2	K562	blood:
3	chr1:159915479..159916369-chr1:159939426..159941106,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11265301	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1316963	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2789424	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789425	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2820555	0.81[ASN][1000 genomes]
rs2820575	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66496035	0.90[ASN][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	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv548055	chr1:159918418-159940000	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159928000-159941800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:159932000-159949800	Weak transcription	Esophagus	oesophagus
3	chr1:159932600-159940800	Weak transcription	Gastric	stomach
4	chr1:159932800-159940800	Weak transcription	Fetal Heart	heart
5	chr1:159933200-159947200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:159933400-159950600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:159935200-159940600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:159935400-159941000	Weak transcription	NHEK	skin
9	chr1:159937400-159947200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:159937600-159944000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:159938000-159943400	Enhancers	Stomach Mucosa	stomach
12	chr1:159938200-159942000	Enhancers	Fetal Intestine Small	intestine
13	chr1:159938200-159943400	Enhancers	Fetal Intestine Large	intestine
14	chr1:159938800-159940200	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr1:159938800-159942200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr1:159939000-159941200	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:159939000-159945200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:159939200-159941200	Enhancers	HepG2	liver
19	chr1:159939400-159942200	Enhancers	Liver	Liver
20	chr1:159939600-159940600	Enhancers	Colonic Mucosa	Colon
21	chr1:159939600-159942000	Enhancers	Pancreas	Pancrea
22	chr1:159939800-159940000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr1:159939800-159941400	Weak transcription	Small Intestine	intestine
24	chr1:159940000-159940600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr1:159940000-159941000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:159940000-159941000	Enhancers	Colon Smooth Muscle	Colon
27	chr1:159940000-159941200	Enhancers	Brain Substantia Nigra	brain
28	chr1:159940000-159941400	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:159940000-159941400	Enhancers	Brain Inferior Temporal Lobe	brain

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