Variant report

Variant	rs11894319
Chromosome Location	chr2:47137267-47137268
allele	A/G
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	chr2:47137094-47137653	HepG2	liver:	n/a	n/a
2	NR3C1	chr2:47136662-47137387	A549	lung:	n/a	n/a
3	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
4	MYC	chr2:47136918-47137286	MCF10A-Er-Src	breast:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
5	SP1	chr2:47136589-47137608	HCT-116	colon:	n/a	n/a
6	POLR2A	chr2:47136622-47137328	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr2:47136751-47137488	U87	brain:	n/a	n/a
8	CBX3	chr2:47136724-47137539	HCT-116	colon:	n/a	n/a
9	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
10	NR3C1	chr2:47136702-47137329	A549	lung:	n/a	n/a
11	TCF12	chr2:47136700-47137443	A549	lung:	n/a	n/a
12	EP300	chr2:47136747-47137448	A549	lung:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
13	CBX3	chr2:47136643-47137521	HCT-116	colon:	n/a	n/a
14	IRF4	chr2:47136777-47137347	GM12878	blood:	n/a	n/a
15	MXI1	chr2:47136434-47137720	IMR90	lung:	n/a	n/a
16	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
17	MAX	chr2:47136714-47137797	HCT-116	colon:	n/a	chr2:47137052-47137061 chr2:47137053-47137062 chr2:47137474-47137485
18	CTCF	chr2:47137120-47137270	NHLF	lung:	n/a	n/a
19	MAX	chr2:47136748-47137397	ECC-1	luminal epithelium:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
20	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
21	POLR2A	chr2:47136766-47137388	U87	brain:	n/a	n/a
22	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
23	EBF1	chr2:47136857-47137292	GM12878	blood:	n/a	n/a
24	MTA3	chr2:47136776-47137331	GM12878	blood:	n/a	n/a
25	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
26	EP300	chr2:47136786-47137803	A549	lung:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
27	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
28	RXRA	chr2:47137181-47137644	HepG2	liver:	n/a	chr2:47137303-47137325 chr2:47137348-47137361 chr2:47137348-47137361 chr2:47137348-47137361
29	TCF7L2	chr2:47136767-47137355	Hela-S3	cervix:	n/a	chr2:47137053-47137062 chr2:47137052-47137061
30	JUN	chr2:47136898-47137303	Hela-S3	cervix:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
31	CTCF	chr2:47137260-47137410	K562	blood:	n/a	n/a
32	MAX	chr2:47136631-47137485	A549	lung:	n/a	chr2:47137052-47137061 chr2:47137053-47137062 chr2:47137474-47137485
33	HNF4A	chr2:47137227-47137531	HepG2	liver:	n/a	chr2:47137346-47137361 chr2:47137348-47137361 chr2:47137346-47137361 chr2:47137368-47137390 chr2:47137346-47137361
34	USF2	chr2:47137094-47137361	Hela-S3	cervix:	n/a	n/a
35	SIN3AK20	chr2:47136595-47137553	HCT-116	colon:	n/a	n/a
36	FOSL1	chr2:47136721-47137418	HCT-116	colon:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
37	FOXM1	chr2:47136843-47137272	GM12878	blood:	n/a	n/a
38	SP1	chr2:47136621-47137614	HCT-116	colon:	n/a	n/a
39	MAX	chr2:47136815-47137318	ECC-1	luminal epithelium:	n/a	chr2:47137052-47137061 chr2:47137053-47137062
40	NR2F2	chr2:47137042-47137801	HepG2	liver:	n/a	n/a
41	POLR2A	chr2:47136823-47137361	HCT-116	colon:	n/a	n/a
42	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
43	PBX3	chr2:47136743-47137359	SK-N-SH	brain:	n/a	n/a
44	JUND	chr2:47136798-47137278	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
45	BATF	chr2:47136803-47137356	GM12878	blood:	n/a	chr2:47137049-47137060 chr2:47137054-47137064
46	RCOR1	chr2:47137230-47137289	HepG2	liver:	n/a	n/a
47	FOSL2	chr2:47136710-47137392	SK-N-SH	brain:	n/a	chr2:47137052-47137061 chr2:47137051-47137063 chr2:47137053-47137061 chr2:47137053-47137062 chr2:47137046-47137058 chr2:47137053-47137060
48	TCF7L2	chr2:47136842-47137367	HCT-116	colon:	n/a	chr2:47137053-47137062 chr2:47137052-47137061
49	POLR2A	chr2:47136773-47137268	HUVEC	blood vessel:	n/a	n/a
50	JUND	chr2:47136655-47137558	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

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: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10164756	0.87[CEU][hapmap]
rs10168851	0.92[EUR][1000 genomes]
rs10174894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197474	0.82[MEX][hapmap]
rs10199965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11890177	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11897050	0.87[CEU][hapmap]
rs13388612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13391660	0.87[CEU][hapmap]
rs13392448	0.91[ASN][1000 genomes]
rs13398851	0.83[ASN][1000 genomes]
rs13406024	0.87[CEU][hapmap]
rs13417753	0.87[CEU][hapmap]
rs13423962	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13424086	0.87[CEU][hapmap]
rs1446499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1446500	0.96[ASN][1000 genomes]
rs17035859	0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs17035867	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs17035878	0.87[CEU][hapmap]
rs17035884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17035887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17035912	0.87[CEU][hapmap]
rs17036060	0.88[CHB][hapmap]
rs2084192	0.96[ASN][1000 genomes]
rs2289927	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289928	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347259	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs28516550	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087857	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34581142	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35433380	1.00[ASN][1000 genomes]
rs4300885	0.87[CEU][hapmap]
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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136825	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136827	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62140550	0.92[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6729569	0.87[CEU][hapmap]
rs6729604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[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	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6755303	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6758093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6758512	0.99[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[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs73926966	0.96[ASN][1000 genomes]
rs754411	0.88[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs7565420	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7574514	0.88[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7574833	0.88[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs7575172	0.96[ASN][1000 genomes]
rs7586004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];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	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];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
rs11894319	MCFD2	cis	Artery Tibial	GTEx
rs11894319	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	chr2:47128200-47138600	Strong transcription	Fetal Thymus	thymus
3	chr2:47129400-47140200	Strong transcription	Placenta	Placenta
4	chr2:47130600-47140800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:47131000-47138400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:47131000-47139800	Strong transcription	Thymus	Thymus
7	chr2:47131000-47140000	Strong transcription	Fetal Intestine Large	intestine
8	chr2:47131000-47140200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:47131000-47140400	Strong transcription	Fetal Stomach	stomach
10	chr2:47131000-47140600	Strong transcription	Fetal Intestine Small	intestine
11	chr2:47131000-47140600	Strong transcription	Fetal Muscle Leg	muscle
12	chr2:47131200-47137600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:47131200-47137800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:47131200-47137800	Strong transcription	Primary hematopoietic stem cells	blood
15	chr2:47131200-47137800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:47131200-47138000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:47131200-47138400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr2:47131200-47140400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:47131200-47141800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:47131400-47137400	Strong transcription	Brain Anterior Caudate	brain
21	chr2:47131400-47138400	Strong transcription	Adipose Nuclei	Adipose
22	chr2:47131400-47140200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:47131400-47142000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:47131600-47138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:47131800-47138000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:47132000-47137600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:47132000-47137800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:47132200-47137400	Strong transcription	Rectal Smooth Muscle	rectum
29	chr2:47132200-47138000	Strong transcription	Dnd41	blood
30	chr2:47132200-47138000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:47132200-47138200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:47132200-47138200	Strong transcription	K562	blood
33	chr2:47132200-47138600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr2:47132200-47139600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:47132400-47137400	Strong transcription	Brain Cingulate Gyrus	brain
36	chr2:47132400-47137600	Strong transcription	Fetal Lung	lung
37	chr2:47132400-47137800	Strong transcription	Primary B cells from cord blood	blood
38	chr2:47132400-47137800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:47132400-47138000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:47132400-47138000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:47132400-47138200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr2:47132400-47138200	Strong transcription	Brain Angular Gyrus	brain
43	chr2:47132400-47138400	Strong transcription	Primary T cells from cord blood	blood
44	chr2:47132400-47138400	Strong transcription	Fetal Brain Female	brain
45	chr2:47132600-47138400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr2:47132800-47138000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:47133000-47138000	Strong transcription	Colonic Mucosa	Colon
48	chr2:47133200-47137600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:47133200-47138200	Strong transcription	Brain Germinal Matrix	brain
50	chr2:47133200-47138200	Strong transcription	Brain Inferior Temporal Lobe	brain

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