Variant report

Variant	rs13398851
Chromosome Location	chr2:47160016-47160017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47157969..47160878-chr2:47166343..47168774,5	K562	blood:
2	chr2:47152236..47154946-chr2:47158648..47161233,3	K562	blood:
3	chr2:47159700..47162383-chr2:47166830..47168688,2	MCF-7	breast:
4	chr2:47142431..47146258-chr2:47159598..47162357,3	K562	blood:
5	chr2:47141885..47146886-chr2:47158240..47162628,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10174894	0.83[ASN][1000 genomes]
rs10199965	0.85[ASN][1000 genomes]
rs11890177	0.85[ASN][1000 genomes]
rs11894319	0.83[ASN][1000 genomes]
rs13388612	0.87[ASN][1000 genomes]
rs13392448	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1446499	0.87[ASN][1000 genomes]
rs1446500	0.87[ASN][1000 genomes]
rs17035884	0.85[ASN][1000 genomes]
rs17035887	0.85[ASN][1000 genomes]
rs2084192	0.87[ASN][1000 genomes]
rs2289927	0.83[ASN][1000 genomes]
rs2289928	0.83[ASN][1000 genomes]
rs28516550	0.85[ASN][1000 genomes]
rs3087857	0.87[ASN][1000 genomes]
rs34581142	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35433380	0.83[ASN][1000 genomes]
rs55872217	0.83[ASN][1000 genomes]
rs56213467	0.83[ASN][1000 genomes]
rs58589709	0.82[ASN][1000 genomes]
rs60194846	0.87[ASN][1000 genomes]
rs62136822	0.85[ASN][1000 genomes]
rs62136823	0.83[ASN][1000 genomes]
rs62136825	0.83[ASN][1000 genomes]
rs62136827	0.83[ASN][1000 genomes]
rs62140550	0.87[ASN][1000 genomes]
rs6544938	0.85[ASN][1000 genomes]
rs6544939	0.85[ASN][1000 genomes]
rs6706031	0.83[ASN][1000 genomes]
rs6715391	0.85[ASN][1000 genomes]
rs6715620	0.87[ASN][1000 genomes]
rs6716381	0.87[ASN][1000 genomes]
rs6722440	0.83[ASN][1000 genomes]
rs6729120	0.87[ASN][1000 genomes]
rs6729604	0.87[ASN][1000 genomes]
rs6733548	0.87[ASN][1000 genomes]
rs6743966	0.85[ASN][1000 genomes]
rs6743994	0.85[ASN][1000 genomes]
rs6755303	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6758093	0.87[ASN][1000 genomes]
rs6758512	0.83[ASN][1000 genomes]
rs71423929	0.87[ASN][1000 genomes]
rs73926966	0.87[ASN][1000 genomes]
rs7575172	0.87[ASN][1000 genomes]
rs7586004	0.85[ASN][1000 genomes]
rs7596198	0.85[ASN][1000 genomes]
rs7601491	0.87[ASN][1000 genomes]
rs8861	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13398851	MCFD2	cis	Adipose Subcutaneous	GTEx
rs13398851	MCFD2	cis	Muscle Skeletal	GTEx
rs13398851	MCFD2	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47144200-47166600	Weak transcription	Pancreas	Pancrea
2	chr2:47144600-47164600	Weak transcription	Spleen	Spleen
3	chr2:47144800-47167000	Weak transcription	Fetal Lung	lung
4	chr2:47146000-47167400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:47150600-47166600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:47150600-47167000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:47151000-47166800	Weak transcription	Small Intestine	intestine
8	chr2:47153400-47164400	Weak transcription	Thymus	Thymus
9	chr2:47153600-47160200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:47153800-47166600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:47154000-47166400	Weak transcription	Hela-S3	cervix
12	chr2:47154400-47163600	Weak transcription	Osteobl	bone
13	chr2:47154400-47166800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:47155200-47164400	Weak transcription	Fetal Thymus	thymus
15	chr2:47155800-47166600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:47157200-47161000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:47157200-47166600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:47157400-47166600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:47159400-47163000	Enhancers	Primary B cells from peripheral blood	blood
20	chr2:47159800-47161600	Enhancers	Primary B cells from cord blood	blood
21	chr2:47160000-47167200	Weak transcription	Fetal Stomach	stomach

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