Variant report

Variant	rs2347259
Chromosome Location	chr2:47127825-47127826
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46654722..46656648-chr2:47126320..47128240,2	K562	blood:
2	chr2:47127180..47130356-chr2:47136713..47140377,4	K562	blood:
3	chr2:47122860..47125506-chr2:47127308..47129361,2	K562	blood:
4	chr2:47127485..47129100-chr2:47135293..47137102,2	MCF-7	breast:
5	chr2:47127542..47131326-chr2:47131677..47134825,5	K562	blood:
6	chr2:47127713..47130924-chr2:47141446..47144583,3	MCF-7	breast:
7	chr2:47114369..47117073-chr2:47127351..47131177,3	K562	blood:
8	chr2:47127370..47129670-chr2:47168001..47169784,2	K562	blood:
9	chr2:47126738..47129144-chr2:47143021..47145167,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000187600	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10174894	0.88[ASN][1000 genomes]
rs10197474	0.86[CHB][hapmap]
rs10199965	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11890177	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11894319	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs13388612	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs13392448	0.83[ASN][1000 genomes]
rs1446499	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1446500	0.88[ASN][1000 genomes]
rs17035859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17035867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs17035884	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs17035887	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2084192	0.88[ASN][1000 genomes]
rs2289927	0.88[ASN][1000 genomes]
rs2289928	0.88[ASN][1000 genomes]
rs28516550	0.94[ASN][1000 genomes]
rs3087857	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs34581142	0.88[ASN][1000 genomes]
rs35433380	0.88[ASN][1000 genomes]
rs4505575	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55872217	0.88[ASN][1000 genomes]
rs56213467	0.85[ASN][1000 genomes]
rs58589709	0.83[ASN][1000 genomes]
rs60088869	0.83[ASN][1000 genomes]
rs60194846	0.88[ASN][1000 genomes]
rs61132855	0.92[ASN][1000 genomes]
rs62136818	0.88[ASN][1000 genomes]
rs62136819	0.88[ASN][1000 genomes]
rs62136820	0.92[ASN][1000 genomes]
rs62136822	0.94[ASN][1000 genomes]
rs62136823	0.88[ASN][1000 genomes]
rs62136825	0.88[ASN][1000 genomes]
rs62136827	0.88[ASN][1000 genomes]
rs62140550	0.88[ASN][1000 genomes]
rs6544938	0.86[ASN][1000 genomes]
rs6544939	0.86[ASN][1000 genomes]
rs6706031	0.88[ASN][1000 genomes]
rs6715391	0.94[ASN][1000 genomes]
rs6715620	0.88[ASN][1000 genomes]
rs6716381	0.88[ASN][1000 genomes]
rs6722440	0.88[ASN][1000 genomes]
rs6729120	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs6729604	0.88[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6733548	0.88[ASN][1000 genomes]
rs6743966	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs6743994	0.94[ASN][1000 genomes]
rs6745578	0.89[JPT][hapmap]
rs6755303	0.88[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs6758093	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs6758512	0.88[ASN][1000 genomes]
rs71423929	0.88[ASN][1000 genomes]
rs7340475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs73926966	0.88[ASN][1000 genomes]
rs754411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7565420	0.83[ASN][1000 genomes]
rs7574514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7574833	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7575172	0.88[ASN][1000 genomes]
rs7586004	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs7596198	0.94[ASN][1000 genomes]
rs7601491	0.88[ASN][1000 genomes]
rs8861	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2347259	MCFD2	cis	Adipose Subcutaneous	GTEx
rs2347259	MCFD2	cis	Artery Tibial	GTEx

Chromatin state (count:80 , 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	chr2:47116200-47128200	Weak transcription	HSMM	muscle
5	chr2:47116200-47128400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:47116200-47128400	Weak transcription	NH-A	brain
7	chr2:47116200-47133000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:47116600-47128000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr2:47116600-47128200	Weak transcription	Fetal Thymus	thymus
10	chr2:47116600-47129600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:47116600-47129800	Weak transcription	Osteobl	bone
12	chr2:47116600-47131000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:47116600-47131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:47116600-47131800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:47116600-47132200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:47116600-47132400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:47116600-47132400	Weak transcription	NHEK	skin
18	chr2:47116800-47131000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:47117400-47133200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:47117800-47131200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:47119600-47140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:47120000-47130800	Weak transcription	Left Ventricle	heart
23	chr2:47120000-47133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:47120800-47133000	Weak transcription	Pancreas	Pancrea
25	chr2:47121000-47132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:47121000-47132400	Weak transcription	Hela-S3	cervix
27	chr2:47121000-47132400	Weak transcription	NHDF-Ad	bronchial
28	chr2:47121200-47129800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:47123600-47131000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:47124200-47131000	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:47124400-47129600	Weak transcription	Primary B cells from cord blood	blood
32	chr2:47124400-47131000	Weak transcription	Fetal Intestine Small	intestine
33	chr2:47124800-47132400	Weak transcription	Fetal Lung	lung
34	chr2:47124800-47132800	Weak transcription	NHLF	lung
35	chr2:47125200-47131000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:47125200-47132200	Weak transcription	Dnd41	blood
37	chr2:47125400-47129800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:47125400-47132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:47125400-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:47125600-47129600	Weak transcription	A549	lung
41	chr2:47125600-47130400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:47125600-47131200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:47125800-47133200	Weak transcription	Spleen	Spleen
44	chr2:47126000-47128200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:47126000-47129600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:47126000-47130200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:47126000-47131400	Weak transcription	Adipose Nuclei	Adipose
48	chr2:47126000-47132600	Weak transcription	HUVEC	blood vessel
49	chr2:47126000-47133200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:47126000-47137000	Weak transcription	Right Atrium	heart

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