Variant report

Variant	rs6733548
Chromosome Location	chr2:47143929-47143930
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:47142367-47144089	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:47140644-47144305	IMR90	lung:	n/a	n/a
3	MXI1	chr2:47140343-47144102	SK-N-SH	brain:	n/a	n/a
4	MXI1	chr2:47140686-47144024	IMR90	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47142780..47146808-chr2:47401206..47405117,7	K562	blood:
2	chr2:47140335..47142832-chr2:47143395..47145229,2	K562	blood:
3	chr2:47140743..47148534-chr2:47401019..47406419,10	MCF-7	breast:
4	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
5	chr2:47143555..47145098-chr2:47147081..47148697,2	K562	blood:
6	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:

No data

Variant related genes	Relation type
MCFD2	TF binding region
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10174894	0.96[ASN][1000 genomes]
rs10199965	0.94[ASN][1000 genomes]
rs11890177	0.94[ASN][1000 genomes]
rs11894319	0.96[ASN][1000 genomes]
rs13388612	1.00[ASN][1000 genomes]
rs13392448	0.94[ASN][1000 genomes]
rs13398851	0.87[ASN][1000 genomes]
rs1446499	1.00[ASN][1000 genomes]
rs1446500	1.00[ASN][1000 genomes]
rs17035859	0.85[ASN][1000 genomes]
rs17035867	0.88[ASN][1000 genomes]
rs17035884	0.94[ASN][1000 genomes]
rs17035887	0.94[ASN][1000 genomes]
rs2084192	1.00[ASN][1000 genomes]
rs2289927	0.96[ASN][1000 genomes]
rs2289928	0.96[ASN][1000 genomes]
rs2347259	0.88[ASN][1000 genomes]
rs28516550	0.94[ASN][1000 genomes]
rs3087857	1.00[ASN][1000 genomes]
rs34581142	0.96[ASN][1000 genomes]
rs35433380	0.96[ASN][1000 genomes]
rs4505575	0.81[ASN][1000 genomes]
rs55872217	0.96[ASN][1000 genomes]
rs56213467	0.96[ASN][1000 genomes]
rs58589709	0.94[ASN][1000 genomes]
rs60194846	1.00[ASN][1000 genomes]
rs61132855	0.88[ASN][1000 genomes]
rs62136818	0.85[ASN][1000 genomes]
rs62136819	0.85[ASN][1000 genomes]
rs62136820	0.88[ASN][1000 genomes]
rs62136822	0.94[ASN][1000 genomes]
rs62136823	0.96[ASN][1000 genomes]
rs62136825	0.96[ASN][1000 genomes]
rs62136827	0.96[ASN][1000 genomes]
rs62140550	1.00[ASN][1000 genomes]
rs62140553	0.84[ASN][1000 genomes]
rs6544938	0.98[ASN][1000 genomes]
rs6544939	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6706031	0.96[ASN][1000 genomes]
rs6715391	0.94[ASN][1000 genomes]
rs6715620	1.00[ASN][1000 genomes]
rs6716381	1.00[ASN][1000 genomes]
rs6722440	0.96[ASN][1000 genomes]
rs6729120	1.00[ASN][1000 genomes]
rs6729604	1.00[ASN][1000 genomes]
rs6743966	0.94[ASN][1000 genomes]
rs6743994	0.94[ASN][1000 genomes]
rs6745578	0.88[ASN][1000 genomes]
rs6755303	0.98[ASN][1000 genomes]
rs6758093	1.00[ASN][1000 genomes]
rs6758512	0.96[ASN][1000 genomes]
rs71423929	1.00[ASN][1000 genomes]
rs7340475	0.88[ASN][1000 genomes]
rs73926966	1.00[ASN][1000 genomes]
rs754411	0.88[ASN][1000 genomes]
rs7565420	0.90[ASN][1000 genomes]
rs7574514	0.85[ASN][1000 genomes]
rs7574833	0.83[ASN][1000 genomes]
rs7575172	1.00[ASN][1000 genomes]
rs7586004	0.94[ASN][1000 genomes]
rs7596198	0.94[ASN][1000 genomes]
rs7601491	1.00[ASN][1000 genomes]
rs8861	0.94[ASN][1000 genomes]
rs9973504	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
rs6733548	MCFD2	Cis_1M	lymphoblastoid	RTeQTL
rs6733548	MCFD2	cis	Muscle Skeletal	GTEx
rs6733548	MCFD2	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47140600-47144400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr2:47141400-47144200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:47141600-47144000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:47141600-47144000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:47141600-47144000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:47141600-47144000	Active TSS	Left Ventricle	heart
7	chr2:47141600-47144200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:47141600-47144200	Active TSS	Pancreas	Pancrea
9	chr2:47141600-47144400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:47141600-47144400	Active TSS	Psoas Muscle	Psoas
11	chr2:47141800-47144200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr2:47141800-47144200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr2:47141800-47144200	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr2:47141800-47144200	Active TSS	Ovary	ovary
15	chr2:47142000-47144000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:47142000-47144000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr2:47142000-47144000	Active TSS	Fetal Intestine Small	intestine
18	chr2:47142000-47144000	Active TSS	GM12878-XiMat	blood
19	chr2:47142000-47144000	Active TSS	K562	blood
20	chr2:47142000-47144000	Active TSS	NHDF-Ad	bronchial
21	chr2:47142000-47144200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr2:47142000-47144200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:47142000-47144200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:47142000-47144200	Active TSS	Fetal Kidney	kidney
25	chr2:47142000-47144200	Active TSS	HSMM	muscle
26	chr2:47142000-47144400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr2:47142000-47144600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:47142200-47144000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:47142200-47144000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:47142200-47144000	Active TSS	Colon Smooth Muscle	Colon
31	chr2:47142200-47144000	Active TSS	Fetal Intestine Large	intestine
32	chr2:47142200-47144000	Active TSS	Fetal Stomach	stomach
33	chr2:47142200-47144000	Active TSS	A549	lung
34	chr2:47142200-47144200	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr2:47142200-47144200	Active TSS	Muscle Satellite Cultured Cells	--
36	chr2:47142200-47144200	Active TSS	Brain Cingulate Gyrus	brain
37	chr2:47142200-47144200	Active TSS	Fetal Lung	lung
38	chr2:47142200-47144200	Active TSS	NHLF	lung
39	chr2:47142200-47144400	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr2:47142200-47144400	Active TSS	Right Ventricle	heart
41	chr2:47142200-47144600	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr2:47142200-47144800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr2:47142400-47144000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:47142400-47144000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:47142400-47144000	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr2:47142400-47144000	Active TSS	Brain Angular Gyrus	brain
47	chr2:47142400-47144000	Active TSS	Brain Anterior Caudate	brain
48	chr2:47142400-47144000	Active TSS	Brain Hippocampus Middle	brain
49	chr2:47142400-47144000	Active TSS	Brain Substantia Nigra	brain
50	chr2:47142400-47144000	Active TSS	Rectal Smooth Muscle	rectum

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