Variant report

Variant	rs2840582
Chromosome Location	chr1:159916937-159916938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr1:159916588-159916953	PFSK-1	brain:	n/a	n/a
2	REST	chr1:159916495-159917033	ECC-1	luminal epithelium:	n/a	chr1:159916543-159916551
3	REST	chr1:159916497-159917023	ECC-1	luminal epithelium:	n/a	chr1:159916543-159916551
4	REST	chr1:159916648-159916998	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:159914809..159917137-chr1:159930388..159932667,2	K562	blood:
2	chr1:159915755..159918019-chr1:159923274..159925459,2	K562	blood:
3	chr1:159916092..159918083-chr1:159956004..159957550,2	MCF-7	breast:
4	chr1:159913973..159917644-chr1:159927852..159934070,11	MCF-7	breast:
5	chr1:159915582..159917480-chr1:159941204..159942730,2	MCF-7	breast:
6	chr1:159914014..159917930-chr1:160000159..160002948,5	MCF-7	breast:

No data

Variant related genes	Relation type
IGSF9	TF binding region
ENSG00000224259	Chromatin interaction
ENSG00000162723	Chromatin interaction
ENSG00000143315	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2249707	0.91[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2789419	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2840584	0.91[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840585	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60669636	0.96[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	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	nsv524006	chr1:159886422-159923111	Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159915800-159919600	Weak transcription	Lung	lung
2	chr1:159916000-159917000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr1:159916000-159917200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:159916000-159918800	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:159916200-159917000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:159916200-159917000	Enhancers	NHEK	skin
7	chr1:159916200-159918000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:159916200-159918800	Weak transcription	K562	blood
9	chr1:159916200-159919000	Weak transcription	A549	lung
10	chr1:159916200-159919800	Enhancers	Fetal Intestine Small	intestine
11	chr1:159916200-159920000	Enhancers	Stomach Mucosa	stomach
12	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
13	chr1:159916400-159917000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:159916600-159917000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:159916600-159918000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:159916600-159918600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:159916600-159918800	Weak transcription	Placenta	Placenta
18	chr1:159916600-159919600	Weak transcription	Colonic Mucosa	Colon
19	chr1:159916600-159920800	Weak transcription	Fetal Lung	lung
20	chr1:159916800-159918600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:159916800-159918800	Weak transcription	Esophagus	oesophagus
22	chr1:159916800-159918800	Weak transcription	Fetal Kidney	kidney
23	chr1:159916800-159918800	Weak transcription	Pancreas	Pancrea
24	chr1:159916800-159919000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:159916800-159919000	Weak transcription	Gastric	stomach
26	chr1:159916800-159919200	Weak transcription	HMEC	breast
27	chr1:159916800-159923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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