Variant report

Variant	rs2840581
Chromosome Location	chr1:159916645-159916646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HA-E2F1	chr1:159915119-159916686	MCF-7	breast:	n/a	chr1:159915640-159915652
2	CTCF	chr1:159916560-159916710	GM12865	blood:	n/a	n/a
3	REST	chr1:159916588-159916953	PFSK-1	brain:	n/a	n/a
4	GATA3	chr1:159915736-159916749	MCF-7	breast:	n/a	chr1:159916047-159916054
5	REST	chr1:159916495-159917033	ECC-1	luminal epithelium:	n/a	chr1:159916543-159916551
6	REST	chr1:159916633-159916928	SK-N-SH	brain:	n/a	n/a
7	REST	chr1:159916497-159917023	ECC-1	luminal epithelium:	n/a	chr1:159916543-159916551
8	CTBP2	chr1:159914761-159916667	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZNF263	chr1:159915248-159916818	HEK293-T-REx	kidney:	n/a	chr1:159915896-159915905 chr1:159915906-159915927 chr1:159915855-159915864

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	chr1:159893029..159897081-chr1:159913897..159916842,4	K562	blood:
5	chr1:159913973..159917644-chr1:159927852..159934070,11	MCF-7	breast:
6	chr1:159915582..159917480-chr1:159941204..159942730,2	MCF-7	breast:
7	chr1:159914014..159917930-chr1:160000159..160002948,5	MCF-7	breast:

Variant related genes	Relation type
IGSF9	TF binding region
ENSG00000143315	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000224259	Chromatin interaction
ENSG00000162723	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2789415	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs2789416	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs2789417	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs2789418	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2820579	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2820584	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs2840583	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs2840586	0.86[AMR][1000 genomes]
rs3001288	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs4297288	0.82[CEU][hapmap]
rs4402127	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159915800-159916800	Enhancers	Esophagus	oesophagus
2	chr1:159915800-159919600	Weak transcription	Lung	lung
3	chr1:159916000-159916800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:159916000-159916800	Enhancers	Gastric	stomach
5	chr1:159916000-159917000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:159916000-159917200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:159916000-159918800	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:159916200-159916800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:159916200-159916800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:159916200-159916800	Enhancers	Pancreas	Pancrea
11	chr1:159916200-159916800	Enhancers	HMEC	breast
12	chr1:159916200-159917000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:159916200-159917000	Enhancers	NHEK	skin
14	chr1:159916200-159918000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:159916200-159918800	Weak transcription	K562	blood
16	chr1:159916200-159919000	Weak transcription	A549	lung
17	chr1:159916200-159919800	Enhancers	Fetal Intestine Small	intestine
18	chr1:159916200-159920000	Enhancers	Stomach Mucosa	stomach
19	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
20	chr1:159916400-159916800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr1:159916400-159916800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:159916400-159916800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:159916400-159916800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:159916400-159916800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:159916400-159916800	Enhancers	Fetal Kidney	kidney
26	chr1:159916400-159917000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:159916600-159916800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:159916600-159916800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr1:159916600-159917000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr1:159916600-159918000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:159916600-159918600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:159916600-159918800	Weak transcription	Placenta	Placenta
33	chr1:159916600-159919600	Weak transcription	Colonic Mucosa	Colon
34	chr1:159916600-159920800	Weak transcription	Fetal Lung	lung

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