Variant report

Variant	rs62136827
Chromosome Location	chr2:47137167-47137168
allele	C/T
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	JUN	chr2:47136904-47137179	HepG2	liver:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
2	SP1	chr2:47137094-47137653	HepG2	liver:	n/a	n/a
3	EP300	chr2:47136890-47137250	GM12878	blood:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
4	NR3C1	chr2:47136662-47137387	A549	lung:	n/a	n/a
5	MAX	chr2:47137016-47137234	A549	lung:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
6	MXI1	chr2:47136940-47137244	Hela-S3	cervix:	n/a	n/a
7	JUND	chr2:47136656-47137500	HCT-116	colon:	n/a	chr2:47137051-47137062 chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
8	MYC	chr2:47136918-47137286	MCF10A-Er-Src	breast:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
9	MAX	chr2:47136897-47137210	Hela-S3	cervix:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
10	NR3C1	chr2:47136846-47137209	ECC-1	luminal epithelium:	n/a	n/a
11	ELK1	chr2:47136910-47137171	Hela-S3	cervix:	n/a	n/a
12	JUND	chr2:47136872-47137255	HepG2	liver:	n/a	chr2:47137051-47137062 chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
13	SP1	chr2:47136589-47137608	HCT-116	colon:	n/a	n/a
14	POLR2A	chr2:47136622-47137328	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr2:47136751-47137488	U87	brain:	n/a	n/a
16	CBX3	chr2:47136724-47137539	HCT-116	colon:	n/a	n/a
17	FOSL2	chr2:47136696-47137467	A549	lung:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
18	SIN3AK20	chr2:47136841-47137224	SK-N-SH	brain:	n/a	n/a
19	FOS	chr2:47136884-47137262	MCF10A-Er-Src	breast:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137051-47137062 chr2:47137053-47137060
20	NR3C1	chr2:47136702-47137329	A549	lung:	n/a	n/a
21	FOS	chr2:47136889-47137235	MCF10A-Er-Src	breast:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137051-47137062 chr2:47137053-47137060
22	TAF1	chr2:47136855-47137170	SK-N-SH	brain:	n/a	n/a
23	TCF12	chr2:47136700-47137443	A549	lung:	n/a	n/a
24	MAZ	chr2:47137027-47137172	GM12878	blood:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
25	REST	chr2:47136725-47137218	PFSK-1	brain:	n/a	chr2:47137065-47137083
26	EP300	chr2:47136747-47137448	A549	lung:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
27	CBX3	chr2:47136643-47137521	HCT-116	colon:	n/a	n/a
28	IRF4	chr2:47136777-47137347	GM12878	blood:	n/a	n/a
29	STAT3	chr2:47137023-47137223	MCF10A-Er-Src	breast:	n/a	chr2:47137053-47137062 chr2:47137052-47137061
30	MYC	chr2:47136905-47137257	MCF10A-Er-Src	breast:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
31	CHD2	chr2:47136937-47137239	Hela-S3	cervix:	n/a	n/a
32	RAD21	chr2:47136919-47137180	Hela-S3	cervix:	n/a	n/a
33	MXI1	chr2:47136434-47137720	IMR90	lung:	n/a	n/a
34	FOS	chr2:47136872-47137270	MCF10A-Er-Src	breast:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137051-47137062 chr2:47137053-47137060
35	MXI1	chr2:47136901-47137225	GM12878	blood:	n/a	n/a
36	MAX	chr2:47136714-47137797	HCT-116	colon:	n/a	chr2:47137052-47137061 chr2:47137053-47137062 chr2:47137474-47137485
37	CTCF	chr2:47137120-47137270	NHLF	lung:	n/a	n/a
38	MAX	chr2:47136748-47137397	ECC-1	luminal epithelium:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
39	POLR2A	chr2:47137101-47137191	MCF10A-Er-Src	breast:	n/a	n/a
40	ZNF143	chr2:47136914-47137227	GM12878	blood:	n/a	n/a
41	JUND	chr2:47136863-47137342	A549	lung:	n/a	chr2:47137051-47137062 chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
42	POLR2A	chr2:47136766-47137388	U87	brain:	n/a	n/a
43	POLR2A	chr2:47135838-47137220	K562	blood:	n/a	n/a
44	FOSL2	chr2:47136845-47137294	SK-N-SH	brain:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
45	EBF1	chr2:47136857-47137292	GM12878	blood:	n/a	n/a
46	MTA3	chr2:47136776-47137331	GM12878	blood:	n/a	n/a
47	FOSL2	chr2:47136864-47137272	A549	lung:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
48	EP300	chr2:47136786-47137803	A549	lung:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
49	FOSL2	chr2:47136818-47137490	HepG2	liver:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
50	TCF7L2	chr2:47136767-47137355	Hela-S3	cervix:	n/a	chr2:47137053-47137062 chr2:47137052-47137061

No.	Distal block	Cell Line	Cell type
1	chr2:47135393..47141252-chr2:47166022..47170880,5	K562	blood:
2	chr2:47135391..47138863-chr2:47402066..47404895,3	K562	blood:
3	chr2:47127180..47130356-chr2:47136713..47140377,4	K562	blood:

Variant related genes	Relation type
MCFD2	TF binding region
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000143933	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	0.89[EUR][1000 genomes]
rs10174894	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199965	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11890177	0.94[ASN][1000 genomes]
rs11894319	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388612	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13392448	0.91[ASN][1000 genomes]
rs13398851	0.83[ASN][1000 genomes]
rs13423962	0.83[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	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2084192	0.96[ASN][1000 genomes]
rs2289927	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289928	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347259	0.88[ASN][1000 genomes]
rs28516550	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087857	0.96[ASN][1000 genomes]
rs34581142	0.82[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	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136825	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62140550	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[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	0.95[AMR][1000 genomes];0.96[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	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729120	0.96[ASN][1000 genomes]
rs6729604	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733548	0.96[ASN][1000 genomes]
rs6743966	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[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	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6758512	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[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	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[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	0.90[AMR][1000 genomes];0.96[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	0.89[AMR][1000 genomes];0.84[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
rs62136827	MCFD2	Cis_1M	lymphoblastoid	RTeQTL
rs62136827	MCFD2	cis	Artery Tibial	GTEx

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	chr2:47128200-47138600	Strong transcription	Fetal Thymus	thymus
3	chr2:47129400-47140200	Strong transcription	Placenta	Placenta
4	chr2:47130200-47137200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:47130600-47140800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:47131000-47138400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:47131000-47139800	Strong transcription	Thymus	Thymus
8	chr2:47131000-47140000	Strong transcription	Fetal Intestine Large	intestine
9	chr2:47131000-47140200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:47131000-47140400	Strong transcription	Fetal Stomach	stomach
11	chr2:47131000-47140600	Strong transcription	Fetal Intestine Small	intestine
12	chr2:47131000-47140600	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:47131200-47137200	Strong transcription	Liver	Liver
14	chr2:47131200-47137600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:47131200-47137800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:47131200-47137800	Strong transcription	Primary hematopoietic stem cells	blood
17	chr2:47131200-47137800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:47131200-47138000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:47131200-47138400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:47131200-47140400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:47131200-47141800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:47131400-47137400	Strong transcription	Brain Anterior Caudate	brain
23	chr2:47131400-47138400	Strong transcription	Adipose Nuclei	Adipose
24	chr2:47131400-47140200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:47131400-47142000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:47131600-47138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:47131800-47137200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:47131800-47137200	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:47131800-47138000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr2:47132000-47137600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:47132000-47137800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:47132200-47137200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr2:47132200-47137400	Strong transcription	Rectal Smooth Muscle	rectum
34	chr2:47132200-47138000	Strong transcription	Dnd41	blood
35	chr2:47132200-47138000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr2:47132200-47138200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr2:47132200-47138200	Strong transcription	K562	blood
38	chr2:47132200-47138600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:47132200-47139600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:47132400-47137400	Strong transcription	Brain Cingulate Gyrus	brain
41	chr2:47132400-47137600	Strong transcription	Fetal Lung	lung
42	chr2:47132400-47137800	Strong transcription	Primary B cells from cord blood	blood
43	chr2:47132400-47137800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:47132400-47138000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:47132400-47138000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:47132400-47138200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr2:47132400-47138200	Strong transcription	Brain Angular Gyrus	brain
48	chr2:47132400-47138400	Strong transcription	Primary T cells from cord blood	blood
49	chr2:47132400-47138400	Strong transcription	Fetal Brain Female	brain
50	chr2:47132600-47138400	Strong transcription	H9 Cell Line	embryonic stem cell

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