Variant report

Variant	rs7574514
Chromosome Location	chr2:47125914-47125915
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10174894	0.84[ASN][1000 genomes]
rs10197474	0.86[CHB][hapmap]
rs10199965	0.89[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11890177	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs11894319	0.88[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs13388612	0.89[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1446499	0.89[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1446500	0.85[ASN][1000 genomes]
rs17035859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17035867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17035884	0.89[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs17035887	0.89[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2084192	0.85[ASN][1000 genomes]
rs2289927	0.84[ASN][1000 genomes]
rs2289928	0.84[ASN][1000 genomes]
rs2347259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28516550	0.90[ASN][1000 genomes]
rs3087857	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs34581142	0.84[ASN][1000 genomes]
rs35433380	0.84[ASN][1000 genomes]
rs4505575	0.96[ASN][1000 genomes]
rs55872217	0.84[ASN][1000 genomes]
rs56213467	0.81[ASN][1000 genomes]
rs60088869	0.84[ASN][1000 genomes]
rs60194846	0.85[ASN][1000 genomes]
rs61132855	0.96[ASN][1000 genomes]
rs62136818	1.00[ASN][1000 genomes]
rs62136819	1.00[ASN][1000 genomes]
rs62136820	0.96[ASN][1000 genomes]
rs62136822	0.90[ASN][1000 genomes]
rs62136823	0.84[ASN][1000 genomes]
rs62136825	0.84[ASN][1000 genomes]
rs62136827	0.84[ASN][1000 genomes]
rs62140550	0.85[ASN][1000 genomes]
rs6544938	0.83[ASN][1000 genomes]
rs6544939	0.83[ASN][1000 genomes]
rs6706031	0.84[ASN][1000 genomes]
rs6715391	0.90[ASN][1000 genomes]
rs6715620	0.85[ASN][1000 genomes]
rs6716381	0.85[ASN][1000 genomes]
rs6722440	0.84[ASN][1000 genomes]
rs6729120	0.89[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6729604	0.89[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs6733548	0.85[ASN][1000 genomes]
rs6743966	0.89[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6743994	0.90[ASN][1000 genomes]
rs6745578	0.91[JPT][hapmap]
rs6755303	0.89[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6758093	0.89[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6758512	0.84[ASN][1000 genomes]
rs71423929	0.85[ASN][1000 genomes]
rs7340475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs73926966	0.85[ASN][1000 genomes]
rs754411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7574833	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7575172	0.85[ASN][1000 genomes]
rs7586004	0.88[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7596198	0.90[ASN][1000 genomes]
rs7601491	0.85[ASN][1000 genomes]
rs8861	0.88[CHB][hapmap];0.89[JPT][hapmap];0.90[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
rs7574514	MCFD2	cis	Artery Tibial	GTEx
rs7574514	MCFD2	Cis_1M	lymphoblastoid	RTeQTL
rs7574514	MCFD2	cis	Muscle Skeletal	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47106400-47131000	Weak transcription	Esophagus	oesophagus
2	chr2:47113200-47131200	Weak transcription	Aorta	Aorta
3	chr2:47116000-47133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:47116200-47127400	Weak transcription	Fetal Stomach	stomach
5	chr2:47116200-47128200	Weak transcription	HSMM	muscle
6	chr2:47116200-47128400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:47116200-47128400	Weak transcription	NH-A	brain
8	chr2:47116200-47133000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:47116600-47128000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:47116600-47128200	Weak transcription	Fetal Thymus	thymus
11	chr2:47116600-47129600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:47116600-47129800	Weak transcription	Osteobl	bone
13	chr2:47116600-47131000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:47116600-47131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:47116600-47131800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:47116600-47132200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:47116600-47132400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:47116600-47132400	Weak transcription	NHEK	skin
19	chr2:47116800-47131000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:47117400-47133200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:47117800-47131200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:47119600-47140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:47120000-47130800	Weak transcription	Left Ventricle	heart
24	chr2:47120000-47133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:47120800-47133000	Weak transcription	Pancreas	Pancrea
26	chr2:47121000-47132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:47121000-47132400	Weak transcription	Hela-S3	cervix
28	chr2:47121000-47132400	Weak transcription	NHDF-Ad	bronchial
29	chr2:47121200-47129800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:47121400-47127200	Weak transcription	K562	blood
31	chr2:47121600-47127600	Weak transcription	Primary T cells from cord blood	blood
32	chr2:47123600-47131000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:47124200-47131000	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:47124400-47129600	Weak transcription	Primary B cells from cord blood	blood
35	chr2:47124400-47131000	Weak transcription	Fetal Intestine Small	intestine
36	chr2:47124800-47132400	Weak transcription	Fetal Lung	lung
37	chr2:47124800-47132800	Weak transcription	NHLF	lung
38	chr2:47125200-47126000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:47125200-47126000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr2:47125200-47131000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:47125200-47132200	Weak transcription	Dnd41	blood
42	chr2:47125400-47129800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:47125400-47132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:47125400-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:47125600-47129600	Weak transcription	A549	lung
46	chr2:47125600-47130400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:47125600-47131200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:47125800-47126000	Enhancers	Adipose Nuclei	Adipose
49	chr2:47125800-47126000	Enhancers	Right Atrium	heart
50	chr2:47125800-47126000	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links