Variant report

Variant	rs11890177
Chromosome Location	chr2:47133055-47133056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47127542..47131326-chr2:47131677..47134825,5	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10174894	0.94[ASN][1000 genomes]
rs10199965	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11894319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13388612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13392448	0.89[ASN][1000 genomes]
rs13398851	0.85[ASN][1000 genomes]
rs1446499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1446500	0.94[ASN][1000 genomes]
rs17035859	0.88[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs17035867	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs17035884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17035887	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17036060	0.88[CHB][hapmap]
rs2084192	0.94[ASN][1000 genomes]
rs2289927	0.94[ASN][1000 genomes]
rs2289928	0.94[ASN][1000 genomes]
rs2347259	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs28516550	1.00[ASN][1000 genomes]
rs3087857	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs34581142	0.94[ASN][1000 genomes]
rs35433380	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4505575	0.86[ASN][1000 genomes]
rs55872217	0.94[ASN][1000 genomes]
rs56213467	0.91[ASN][1000 genomes]
rs58589709	0.89[ASN][1000 genomes]
rs60194846	0.94[ASN][1000 genomes]
rs61132855	0.94[ASN][1000 genomes]
rs62136818	0.90[ASN][1000 genomes]
rs62136819	0.90[ASN][1000 genomes]
rs62136820	0.94[ASN][1000 genomes]
rs62136822	1.00[ASN][1000 genomes]
rs62136823	0.94[ASN][1000 genomes]
rs62136825	0.94[ASN][1000 genomes]
rs62136827	0.94[ASN][1000 genomes]
rs62140550	0.94[ASN][1000 genomes]
rs6544938	0.92[ASN][1000 genomes]
rs6544939	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6706031	0.94[ASN][1000 genomes]
rs6715391	1.00[ASN][1000 genomes]
rs6715620	0.94[ASN][1000 genomes]
rs6716381	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6722440	0.94[ASN][1000 genomes]
rs6729120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6729604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6733548	0.94[ASN][1000 genomes]
rs6743966	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6743994	1.00[ASN][1000 genomes]
rs6745578	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6755303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6758093	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs6758512	0.94[ASN][1000 genomes]
rs71423929	0.94[ASN][1000 genomes]
rs7340475	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs73926966	0.94[ASN][1000 genomes]
rs754411	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs7565420	0.89[ASN][1000 genomes]
rs7574514	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs7574833	0.83[ASW][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]
rs7575172	0.94[ASN][1000 genomes]
rs7586004	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7596198	1.00[ASN][1000 genomes]
rs7601491	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8861	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9973504	0.85[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11890177	AC016722.4	cis	Muscle Skeletal	GTEx
rs11890177	MCFD2	cis	Adipose Subcutaneous	GTEx
rs11890177	MCFD2	cis	Artery Aorta	GTEx
rs11890177	MCFD2	Cis_1M	lymphoblastoid	RTeQTL
rs11890177	MCFD2	cis	Artery Tibial	GTEx
rs11890177	MCFD2	cis	multi-tissue	Pritchard
rs11890177	MCFD2	cis	lung	GTEx
rs11890177	MCFD2	cis	cerebellum	SCAN
rs11890177	MCFD2	cis	Heart Left Ventricle	GTEx
rs11890177	MCFD2	cis	Esophagus Muscularis	GTEx
rs11890177	MCFD2	cis	parietal	SCAN
rs11890177	MCFD2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47116000-47133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:47117400-47133200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:47119600-47140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:47120000-47133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:47125800-47133200	Weak transcription	Spleen	Spleen
6	chr2:47126000-47133200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:47126000-47137000	Weak transcription	Right Atrium	heart
8	chr2:47127200-47133200	Weak transcription	Brain Germinal Matrix	brain
9	chr2:47127600-47134600	Weak transcription	Fetal Brain Male	brain
10	chr2:47128200-47138600	Strong transcription	Fetal Thymus	thymus
11	chr2:47128600-47133200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:47129200-47133200	Weak transcription	Ovary	ovary
13	chr2:47129400-47140200	Strong transcription	Placenta	Placenta
14	chr2:47129600-47137000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:47129800-47135200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:47129800-47136200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:47129800-47136400	Strong transcription	Osteobl	bone
18	chr2:47130000-47133400	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:47130200-47136000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:47130200-47137200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:47130600-47133200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:47130600-47134000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:47130600-47134000	Weak transcription	Fetal Kidney	kidney
24	chr2:47130600-47140800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:47130800-47136000	Strong transcription	Left Ventricle	heart
26	chr2:47130800-47136800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:47131000-47133200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:47131000-47134000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:47131000-47136000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:47131000-47136000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:47131000-47136000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:47131000-47136000	Strong transcription	NH-A	brain
33	chr2:47131000-47136200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:47131000-47136400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:47131000-47136600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:47131000-47136600	Weak transcription	Stomach Mucosa	stomach
37	chr2:47131000-47138400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:47131000-47139800	Strong transcription	Thymus	Thymus
39	chr2:47131000-47140000	Strong transcription	Fetal Intestine Large	intestine
40	chr2:47131000-47140200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:47131000-47140400	Strong transcription	Fetal Stomach	stomach
42	chr2:47131000-47140600	Strong transcription	Fetal Intestine Small	intestine
43	chr2:47131000-47140600	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:47131200-47135800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:47131200-47136600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:47131200-47136600	Strong transcription	Brain Hippocampus Middle	brain
47	chr2:47131200-47136800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:47131200-47137200	Strong transcription	Liver	Liver
49	chr2:47131200-47137600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:47131200-47137800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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