Variant report

Variant	rs11925267
Chromosome Location	chr3:111601843-111601844
allele	C/T
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	EP300	chr3:111601725-111601904	GM12878	blood:	n/a	n/a
2	MEF2A	chr3:111601693-111601951	GM12878	blood:	n/a	chr3:111601840-111601856 chr3:111601840-111601855 chr3:111601843-111601852 chr3:111601839-111601855 chr3:111601842-111601853
3	RUNX3	chr3:111601565-111602043	GM12878	blood:	n/a	n/a
4	RUNX3	chr3:111601632-111601975	GM12878	blood:	n/a	n/a
5	SPI1	chr3:111601655-111601882	GM12891	blood:	n/a	n/a
6	MEF2A	chr3:111601548-111602022	GM12878	blood:	n/a	chr3:111601840-111601856 chr3:111601840-111601855 chr3:111601843-111601852 chr3:111601839-111601855 chr3:111601842-111601853

Variant related genes	Relation type
PHLDB2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11916434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11916823	0.81[AFR][1000 genomes]
rs11919057	0.85[YRI][hapmap]
rs11919759	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11922755	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11924354	1.00[ASW][hapmap]
rs11929116	1.00[AMR][1000 genomes]
rs11929149	1.00[AMR][1000 genomes]
rs4277659	1.00[AMR][1000 genomes]
rs4396865	1.00[AMR][1000 genomes]
rs4464420	1.00[AMR][1000 genomes]
rs4603931	1.00[AMR][1000 genomes]
rs58052524	1.00[AMR][1000 genomes]
rs6438010	1.00[AMR][1000 genomes]
rs6438011	1.00[AMR][1000 genomes]
rs73852747	1.00[AMR][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	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv980070	chr3:111592547-111602240	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11925267	FFAR1	trans	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111584600-111603400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:111585200-111622000	Weak transcription	HSMMtube	muscle
3	chr3:111585400-111603400	Weak transcription	Spleen	Spleen
4	chr3:111585400-111609000	Weak transcription	Esophagus	oesophagus
5	chr3:111587200-111603000	Weak transcription	Placenta	Placenta
6	chr3:111589200-111603400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:111589800-111603400	Weak transcription	Pancreas	Pancrea
8	chr3:111591600-111603200	Weak transcription	Ovary	ovary
9	chr3:111591600-111603600	Weak transcription	HepG2	liver
10	chr3:111591600-111610600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:111591600-111633200	Weak transcription	Fetal Kidney	kidney
12	chr3:111593600-111603000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:111593600-111603000	Weak transcription	Lung	lung
14	chr3:111593600-111603200	Weak transcription	Gastric	stomach
15	chr3:111593600-111603400	Weak transcription	HSMM	muscle
16	chr3:111593600-111608800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:111593800-111602000	Weak transcription	HUVEC	blood vessel
18	chr3:111593800-111602800	Weak transcription	NHLF	lung
19	chr3:111593800-111603000	Weak transcription	Fetal Stomach	stomach
20	chr3:111593800-111603200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:111593800-111603400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:111594000-111603400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:111594400-111603200	Weak transcription	HMEC	breast
24	chr3:111595400-111602600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:111598400-111612600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:111599200-111603400	Weak transcription	Right Atrium	heart
27	chr3:111599400-111603600	Weak transcription	NH-A	brain
28	chr3:111599600-111602400	Weak transcription	Hela-S3	cervix
29	chr3:111599600-111603000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:111599600-111603000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:111600200-111602800	Weak transcription	Liver	Liver
32	chr3:111600200-111603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:111600200-111603000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:111600200-111604000	Weak transcription	A549	lung
35	chr3:111600400-111602000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:111600400-111602600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:111600400-111603200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:111600400-111603400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:111600400-111603600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:111600600-111603000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:111600600-111603000	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:111600600-111603200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:111600600-111603200	Weak transcription	Fetal Intestine Small	intestine
44	chr3:111600600-111603400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:111601200-111602400	Enhancers	Colon Smooth Muscle	Colon
46	chr3:111601200-111602800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:111601200-111603200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:111601200-111612400	Strong transcription	NHEK	skin
49	chr3:111601400-111603200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:111601600-111602400	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links