Variant report

Variant	rs62136825
Chromosome Location	chr2:47136617-47136618
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr2:47136589-47137608	HCT-116	colon:	n/a	n/a
2	MXI1	chr2:47136434-47137720	IMR90	lung:	n/a	n/a
3	POLR2A	chr2:47135838-47137220	K562	blood:	n/a	n/a
4	SIN3AK20	chr2:47136595-47137553	HCT-116	colon:	n/a	n/a
5	FOSL1	chr2:47136610-47137778	HCT-116	colon:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
6	GATA3	chr2:47136560-47137656	A549	lung:	n/a	chr2:47137051-47137060 chr2:47137314-47137321 chr2:47136670-47136677
7	JUND	chr2:47136511-47137441	GM12878	blood:	n/a	chr2:47137051-47137062 chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
8	EP300	chr2:47136604-47137452	ECC-1	luminal epithelium:	n/a	chr2:47137052-47137061 chr2:47137053-47137062

No.	Distal block	Cell Line	Cell type
1	chr2:47135393..47141252-chr2:47166022..47170880,5	K562	blood:
2	chr2:46925509..46928130-chr2:47135510..47137063,2	MCF-7	breast:
3	chr2:47135391..47138863-chr2:47402066..47404895,3	K562	blood:

Variant related genes	Relation type
MCFD2	TF binding region
ENSG00000143933	Chromatin interaction
ENSG00000171150	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10168851	0.92[EUR][1000 genomes]
rs10174894	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199965	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11890177	0.94[ASN][1000 genomes]
rs11894319	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388612	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13392448	0.91[ASN][1000 genomes]
rs13398851	0.83[ASN][1000 genomes]
rs13423962	0.87[EUR][1000 genomes]
rs1446499	0.96[ASN][1000 genomes]
rs1446500	0.96[ASN][1000 genomes]
rs17035859	0.84[ASN][1000 genomes]
rs17035867	0.88[ASN][1000 genomes]
rs17035884	0.94[ASN][1000 genomes]
rs17035887	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2084192	0.96[ASN][1000 genomes]
rs2289927	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289928	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347259	0.88[ASN][1000 genomes]
rs28516550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087857	0.96[ASN][1000 genomes]
rs34581142	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35433380	1.00[ASN][1000 genomes]
rs4505575	0.80[ASN][1000 genomes]
rs55872217	1.00[ASN][1000 genomes]
rs56213467	0.92[ASN][1000 genomes]
rs58589709	0.91[ASN][1000 genomes]
rs60194846	0.96[ASN][1000 genomes]
rs61132855	0.88[ASN][1000 genomes]
rs62136818	0.84[ASN][1000 genomes]
rs62136819	0.84[ASN][1000 genomes]
rs62136820	0.88[ASN][1000 genomes]
rs62136822	0.94[ASN][1000 genomes]
rs62136823	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136827	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62140550	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62140553	0.80[ASN][1000 genomes]
rs6544938	0.98[ASN][1000 genomes]
rs6544939	0.98[ASN][1000 genomes]
rs6706031	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715391	0.94[ASN][1000 genomes]
rs6715620	0.96[ASN][1000 genomes]
rs6716381	0.96[ASN][1000 genomes]
rs6722440	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729120	0.96[ASN][1000 genomes]
rs6729604	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733548	0.96[ASN][1000 genomes]
rs6743966	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6743994	0.94[ASN][1000 genomes]
rs6745578	0.85[ASN][1000 genomes]
rs6755303	0.94[ASN][1000 genomes]
rs6758093	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6758512	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423929	0.96[ASN][1000 genomes]
rs7340475	0.88[ASN][1000 genomes]
rs73926966	0.96[ASN][1000 genomes]
rs754411	0.92[ASN][1000 genomes]
rs7565420	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7574514	0.84[ASN][1000 genomes]
rs7574833	0.86[ASN][1000 genomes]
rs7575172	0.96[ASN][1000 genomes]
rs7586004	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7596198	0.94[ASN][1000 genomes]
rs7601491	0.96[ASN][1000 genomes]
rs8861	0.94[ASN][1000 genomes]
rs9973504	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[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
rs62136825	MCFD2	cis	Artery Tibial	GTEx
rs62136825	MCFD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47119600-47140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:47126000-47137000	Weak transcription	Right Atrium	heart
3	chr2:47128200-47138600	Strong transcription	Fetal Thymus	thymus
4	chr2:47129400-47140200	Strong transcription	Placenta	Placenta
5	chr2:47129600-47137000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:47130200-47137200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:47130600-47140800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:47130800-47136800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:47131000-47138400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:47131000-47139800	Strong transcription	Thymus	Thymus
11	chr2:47131000-47140000	Strong transcription	Fetal Intestine Large	intestine
12	chr2:47131000-47140200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:47131000-47140400	Strong transcription	Fetal Stomach	stomach
14	chr2:47131000-47140600	Strong transcription	Fetal Intestine Small	intestine
15	chr2:47131000-47140600	Strong transcription	Fetal Muscle Leg	muscle
16	chr2:47131200-47136800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:47131200-47137200	Strong transcription	Liver	Liver
18	chr2:47131200-47137600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:47131200-47137800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:47131200-47137800	Strong transcription	Primary hematopoietic stem cells	blood
21	chr2:47131200-47137800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:47131200-47138000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:47131200-47138400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr2:47131200-47140400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:47131200-47141800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:47131400-47137400	Strong transcription	Brain Anterior Caudate	brain
27	chr2:47131400-47138400	Strong transcription	Adipose Nuclei	Adipose
28	chr2:47131400-47140200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:47131400-47142000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:47131600-47138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:47131800-47137000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:47131800-47137000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr2:47131800-47137200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:47131800-47137200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:47131800-47138000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:47132000-47137600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:47132000-47137800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:47132200-47137200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr2:47132200-47137400	Strong transcription	Rectal Smooth Muscle	rectum
40	chr2:47132200-47138000	Strong transcription	Dnd41	blood
41	chr2:47132200-47138000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:47132200-47138200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr2:47132200-47138200	Strong transcription	K562	blood
44	chr2:47132200-47138600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:47132200-47139600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:47132400-47137000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr2:47132400-47137400	Strong transcription	Brain Cingulate Gyrus	brain
48	chr2:47132400-47137600	Strong transcription	Fetal Lung	lung
49	chr2:47132400-47137800	Strong transcription	Primary B cells from cord blood	blood
50	chr2:47132400-47137800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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