Variant report

Variant	rs2289928
Chromosome Location	chr2:47134904-47134905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10164756	0.87[CEU][hapmap]
rs10168851	0.92[EUR][1000 genomes]
rs10174894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197474	0.82[MEX][hapmap]
rs10199965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11890177	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11894319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897050	0.87[CEU][hapmap]
rs13388612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13391660	0.87[CEU][hapmap]
rs13392448	0.91[ASN][1000 genomes]
rs13398851	0.83[ASN][1000 genomes]
rs13406024	0.87[CEU][hapmap]
rs13417753	0.87[CEU][hapmap]
rs13423962	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13424086	0.87[CEU][hapmap]
rs1446499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1446500	0.96[ASN][1000 genomes]
rs17035859	0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs17035867	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs17035878	0.87[CEU][hapmap]
rs17035884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17035887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17035912	0.87[CEU][hapmap]
rs17036060	0.88[CHB][hapmap]
rs2084192	0.96[ASN][1000 genomes]
rs2289927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347259	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs28516550	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087857	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34581142	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35433380	1.00[ASN][1000 genomes]
rs4300885	0.87[CEU][hapmap]
rs4505575	0.80[ASN][1000 genomes]
rs55872217	1.00[ASN][1000 genomes]
rs56213467	0.92[ASN][1000 genomes]
rs58589709	0.91[ASN][1000 genomes]
rs60194846	0.96[ASN][1000 genomes]
rs61132855	0.88[ASN][1000 genomes]
rs62136818	0.84[ASN][1000 genomes]
rs62136819	0.84[ASN][1000 genomes]
rs62136820	0.88[ASN][1000 genomes]
rs62136822	0.94[ASN][1000 genomes]
rs62136823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136825	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136827	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62140550	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62140553	0.80[ASN][1000 genomes]
rs6544938	0.98[ASN][1000 genomes]
rs6544939	0.98[ASN][1000 genomes]
rs6706031	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715391	0.94[ASN][1000 genomes]
rs6715620	0.96[ASN][1000 genomes]
rs6716381	0.96[ASN][1000 genomes]
rs6722440	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6729569	0.87[CEU][hapmap]
rs6729604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733548	0.96[ASN][1000 genomes]
rs6743966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6743994	0.94[ASN][1000 genomes]
rs6745578	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6755303	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6758093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6758512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423929	0.96[ASN][1000 genomes]
rs7340475	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs73926966	0.96[ASN][1000 genomes]
rs754411	0.88[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs7565420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7574514	0.88[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7574833	0.88[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs7575172	0.96[ASN][1000 genomes]
rs7586004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7596198	0.94[ASN][1000 genomes]
rs7601491	0.96[ASN][1000 genomes]
rs8861	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs9973504	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2289928	MCFD2	cis	multi-tissue	Pritchard
rs2289928	MCFD2	cis	Artery Tibial	GTEx
rs2289928	MCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47119600-47140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:47126000-47137000	Weak transcription	Right Atrium	heart
3	chr2:47128200-47138600	Strong transcription	Fetal Thymus	thymus
4	chr2:47129400-47140200	Strong transcription	Placenta	Placenta
5	chr2:47129600-47137000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:47129800-47135200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:47129800-47136200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:47129800-47136400	Strong transcription	Osteobl	bone
9	chr2:47130200-47136000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:47130200-47137200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:47130600-47140800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:47130800-47136000	Strong transcription	Left Ventricle	heart
13	chr2:47130800-47136800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:47131000-47136000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:47131000-47136000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:47131000-47136000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:47131000-47136000	Strong transcription	NH-A	brain
18	chr2:47131000-47136200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:47131000-47136400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr2:47131000-47136600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:47131000-47136600	Weak transcription	Stomach Mucosa	stomach
22	chr2:47131000-47138400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:47131000-47139800	Strong transcription	Thymus	Thymus
24	chr2:47131000-47140000	Strong transcription	Fetal Intestine Large	intestine
25	chr2:47131000-47140200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:47131000-47140400	Strong transcription	Fetal Stomach	stomach
27	chr2:47131000-47140600	Strong transcription	Fetal Intestine Small	intestine
28	chr2:47131000-47140600	Strong transcription	Fetal Muscle Leg	muscle
29	chr2:47131200-47135800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:47131200-47136600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:47131200-47136600	Strong transcription	Brain Hippocampus Middle	brain
32	chr2:47131200-47136800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:47131200-47137200	Strong transcription	Liver	Liver
34	chr2:47131200-47137600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:47131200-47137800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:47131200-47137800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr2:47131200-47137800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:47131200-47138000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:47131200-47138400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:47131200-47140400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:47131200-47141800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:47131400-47137400	Strong transcription	Brain Anterior Caudate	brain
43	chr2:47131400-47138400	Strong transcription	Adipose Nuclei	Adipose
44	chr2:47131400-47140200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:47131400-47142000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr2:47131600-47138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:47131800-47136400	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr2:47131800-47137000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:47131800-47137000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr2:47131800-47137200	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links