Variant report

Variant	rs28516550
Chromosome Location	chr2:47131909-47131910
allele	C/G
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:
2	chr2:47130325..47132416-chr2:47141397..47144318,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10168851	0.92[EUR][1000 genomes]
rs10174894	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10199965	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890177	1.00[ASN][1000 genomes]
rs11894319	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13388612	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13392448	0.89[ASN][1000 genomes]
rs13398851	0.85[ASN][1000 genomes]
rs13423962	0.87[EUR][1000 genomes]
rs1446499	0.94[ASN][1000 genomes]
rs1446500	0.94[ASN][1000 genomes]
rs17035859	0.90[ASN][1000 genomes]
rs17035867	0.94[ASN][1000 genomes]
rs17035884	1.00[ASN][1000 genomes]
rs17035887	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084192	0.94[ASN][1000 genomes]
rs2289927	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289928	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2347259	0.94[ASN][1000 genomes]
rs3087857	0.94[ASN][1000 genomes]
rs34581142	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35433380	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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136825	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136827	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62140550	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544938	0.92[ASN][1000 genomes]
rs6544939	0.92[ASN][1000 genomes]
rs6706031	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715391	1.00[ASN][1000 genomes]
rs6715620	0.94[ASN][1000 genomes]
rs6716381	0.94[ASN][1000 genomes]
rs6722440	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6729120	0.94[ASN][1000 genomes]
rs6729604	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6733548	0.94[ASN][1000 genomes]
rs6743966	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743994	1.00[ASN][1000 genomes]
rs6745578	0.83[ASN][1000 genomes]
rs6755303	0.92[ASN][1000 genomes]
rs6758093	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6758512	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71423929	0.94[ASN][1000 genomes]
rs7340475	0.94[ASN][1000 genomes]
rs73926966	0.94[ASN][1000 genomes]
rs754411	0.94[ASN][1000 genomes]
rs7565420	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7574514	0.90[ASN][1000 genomes]
rs7574833	0.88[ASN][1000 genomes]
rs7575172	0.94[ASN][1000 genomes]
rs7586004	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596198	1.00[ASN][1000 genomes]
rs7601491	0.94[ASN][1000 genomes]
rs8861	1.00[ASN][1000 genomes]
rs9973504	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28516550	MCFD2	cis	Artery Tibial	GTEx
rs28516550	MCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr2:47116200-47133000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:47116600-47132200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:47116600-47132400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:47116600-47132400	Weak transcription	NHEK	skin
6	chr2:47117400-47133200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:47119600-47140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:47120000-47133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:47120800-47133000	Weak transcription	Pancreas	Pancrea
10	chr2:47121000-47132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:47121000-47132400	Weak transcription	Hela-S3	cervix
12	chr2:47121000-47132400	Weak transcription	NHDF-Ad	bronchial
13	chr2:47124800-47132400	Weak transcription	Fetal Lung	lung
14	chr2:47124800-47132800	Weak transcription	NHLF	lung
15	chr2:47125200-47132200	Weak transcription	Dnd41	blood
16	chr2:47125400-47132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:47125400-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:47125800-47133200	Weak transcription	Spleen	Spleen
19	chr2:47126000-47132600	Weak transcription	HUVEC	blood vessel
20	chr2:47126000-47133200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:47126000-47137000	Weak transcription	Right Atrium	heart
22	chr2:47126400-47132400	Weak transcription	Lung	lung
23	chr2:47126400-47132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:47126800-47132200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr2:47127000-47132200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:47127200-47132400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:47127200-47132800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:47127200-47133200	Weak transcription	Brain Germinal Matrix	brain
29	chr2:47127400-47132000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:47127400-47132200	Weak transcription	Right Ventricle	heart
31	chr2:47127600-47134600	Weak transcription	Fetal Brain Male	brain
32	chr2:47128200-47132400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:47128200-47138600	Strong transcription	Fetal Thymus	thymus
34	chr2:47128400-47132400	Weak transcription	Primary T cells from cord blood	blood
35	chr2:47128600-47132800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:47128600-47133200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:47128800-47132200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:47128800-47132600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:47129200-47132000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:47129200-47133200	Weak transcription	Ovary	ovary
41	chr2:47129400-47132200	Weak transcription	HSMM	muscle
42	chr2:47129400-47132400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:47129400-47140200	Strong transcription	Placenta	Placenta
44	chr2:47129600-47132400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:47129600-47133000	Weak transcription	Gastric	stomach
46	chr2:47129600-47137000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:47129800-47132600	Weak transcription	HMEC	breast
48	chr2:47129800-47135200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:47129800-47136200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:47129800-47136400	Strong transcription	Osteobl	bone

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