Variant report

Variant	rs2840588
Chromosome Location	chr1:159931395-159931396
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:159926244..159929298-chr1:159931208..159934136,4	K562	blood:
2	chr1:159914809..159917137-chr1:159930388..159932667,2	K562	blood:
3	chr1:159913973..159917644-chr1:159927852..159934070,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11591079	1.00[CHB][hapmap]
rs1320570	1.00[CHB][hapmap]
rs17427209	1.00[CHB][hapmap]
rs17467492	1.00[CHB][hapmap]
rs2789415	1.00[CHB][hapmap];0.81[GIH][hapmap]
rs2789416	1.00[CHB][hapmap];0.81[GIH][hapmap]
rs2789417	1.00[CHB][hapmap];0.81[GIH][hapmap]
rs2789418	1.00[CHB][hapmap]
rs2820579	1.00[CHB][hapmap]
rs2820584	1.00[CHB][hapmap]
rs2840583	1.00[CHB][hapmap];0.81[GIH][hapmap]
rs3001288	1.00[CHB][hapmap]
rs6662675	1.00[CHB][hapmap]
rs6662918	1.00[CHB][hapmap]

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	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
3	nsv520773	chr1:159922959-159935569	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159928000-159931800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:159928000-159941800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:159928200-159931400	Enhancers	K562	blood
4	chr1:159928800-159931400	Enhancers	Esophagus	oesophagus
5	chr1:159929000-159931600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:159929400-159934000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:159930600-159931600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:159930600-159931600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:159930600-159931600	Enhancers	Ovary	ovary
10	chr1:159930600-159932200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:159930600-159932400	Active TSS	NHEK	skin
12	chr1:159930800-159931600	Enhancers	Fetal Lung	lung
13	chr1:159930800-159931600	Flanking Active TSS	Osteobl	bone
14	chr1:159930800-159932200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:159930800-159933000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:159931000-159931400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:159931000-159931400	Enhancers	Gastric	stomach
18	chr1:159931000-159931600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:159931000-159931600	Flanking Active TSS	Fetal Intestine Small	intestine
20	chr1:159931000-159931600	Flanking Active TSS	HSMM	muscle
21	chr1:159931000-159931600	Active TSS	NHDF-Ad	bronchial
22	chr1:159931000-159931800	Active TSS	Fetal Muscle Trunk	muscle
23	chr1:159931000-159932000	Active TSS	Fetal Muscle Leg	muscle
24	chr1:159931000-159932200	Active TSS	Adipose Nuclei	Adipose
25	chr1:159931000-159932400	Active TSS	Colonic Mucosa	Colon
26	chr1:159931000-159932400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:159931000-159932600	Active TSS	Duodenum Mucosa	Duodenum
28	chr1:159931000-159932600	Active TSS	Fetal Stomach	stomach
29	chr1:159931000-159934400	Active TSS	Stomach Mucosa	stomach
30	chr1:159931200-159931400	Enhancers	Fetal Intestine Large	intestine
31	chr1:159931200-159931400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr1:159931200-159931400	Enhancers	HMEC	breast
33	chr1:159931200-159931600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:159931200-159931600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:159931200-159931600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr1:159931200-159931600	Active TSS	NHLF	lung
37	chr1:159931200-159932200	Active TSS	Rectal Smooth Muscle	rectum

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