Variant report

Variant	rs6755386
Chromosome Location	chr2:47168892-47168893
allele	C/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	RAD21	chr2:47168551-47169370	A549	lung:	n/a	n/a
2	CTCF	chr2:47168800-47168950	HAc	cerebellar:	n/a	chr2:47168914-47168927
3	HEY1	chr2:47168610-47169265	HepG2	liver:	n/a	n/a
4	CTCF	chr2:47168880-47169030	HCPEpiC	choroid plexus:	n/a	chr2:47168914-47168927
5	CTCF	chr2:47168820-47168970	HRPEpiC	eye:	n/a	chr2:47168914-47168927
6	RELA	chr2:47168667-47169932	GM19193	blood:	n/a	n/a
7	TAF1	chr2:47168660-47169118	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr2:47168800-47168950	Hela-S3	cervix:	n/a	chr2:47168914-47168927
9	CTCF	chr2:47168780-47168930	GM12874	blood:	n/a	chr2:47168914-47168927
10	CHD1	chr2:47168694-47169296	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F4	chr2:47167993-47169602	K562	blood:	n/a	chr2:47169461-47169468 chr2:47168901-47168909 chr2:47168899-47168910 chr2:47169461-47169468 chr2:47168108-47168120 chr2:47168958-47168968 chr2:47169457-47169469 chr2:47169461-47169468
12	CTCF	chr2:47168840-47168990	HRPEpiC	eye:	n/a	chr2:47168914-47168927
13	POLR2A	chr2:47168048-47169610	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:47168835-47169161	K562	blood:	n/a	n/a
15	POLR2A	chr2:47168038-47169209	K562	blood:	n/a	n/a
16	TCF3	chr2:47168108-47169060	GM12878	blood:	n/a	n/a
17	CTCF	chr2:47168800-47168950	GM12864	blood:	n/a	chr2:47168914-47168927
18	CTCF	chr2:47168800-47168950	GM12871	blood:	n/a	chr2:47168914-47168927
19	POLR2A	chr2:47168245-47169855	GM12892	blood:	n/a	n/a
20	MAX	chr2:47168564-47169187	SK-N-SH	brain:	n/a	chr2:47169037-47169048
21	TAF1	chr2:47168110-47169018	HepG2	liver:	n/a	n/a
22	TCF12	chr2:47168679-47169018	GM12878	blood:	n/a	n/a
23	CREB1	chr2:47167831-47169080	A549	lung:	n/a	chr2:47168009-47168022
24	TBP	chr2:47168783-47169900	GM12878	blood:	n/a	n/a
25	E2F6	chr2:47168563-47169108	K562	blood:	n/a	chr2:47168901-47168909 chr2:47168958-47168968
26	ZBTB7A	chr2:47167467-47169239	ECC-1	luminal epithelium:	n/a	n/a
27	STAT3	chr2:47168740-47169082	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr2:47167996-47169186	K562	blood:	n/a	n/a
29	POLR2A	chr2:47167706-47169478	HUVEC	blood vessel:	n/a	n/a
30	YY1	chr2:47168081-47169510	GM12892	blood:	n/a	chr2:47168670-47168690 chr2:47168245-47168259 chr2:47168676-47168688
31	RCOR1	chr2:47168725-47169405	Hela-S3	cervix:	n/a	n/a
32	MAX	chr2:47167603-47169355	K562	blood:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
33	CTCF	chr2:47168880-47169030	HCM	heart:	n/a	chr2:47168914-47168927
34	MAX	chr2:47168615-47169131	A549	lung:	n/a	chr2:47169037-47169048
35	ZNF143	chr2:47168853-47169103	K562	blood:	n/a	n/a
36	CTCF	chr2:47168860-47169010	HMEC	breast:	n/a	chr2:47168914-47168927
37	CTCF	chr2:47168780-47168930	GM12872	blood:	n/a	chr2:47168914-47168927
38	POLR2A	chr2:47167805-47169022	A549	lung:	n/a	n/a
39	RUNX3	chr2:47168562-47169995	GM12878	blood:	n/a	chr2:47169041-47169056
40	MYC	chr2:47167697-47169785	NB4	blood:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
41	EP300	chr2:47168724-47169035	GM12878	blood:	n/a	chr2:47168948-47168964
42	CHD2	chr2:47168605-47169105	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr2:47168880-47169030	HCFaa	heart:	n/a	chr2:47168914-47168927
44	ELF1	chr2:47168697-47169137	K562	blood:	n/a	n/a
45	POLR2A	chr2:47168032-47169485	MCF-7	breast:	n/a	n/a
46	YY1	chr2:47168548-47168981	GM12891	blood:	n/a	chr2:47168670-47168690 chr2:47168676-47168688
47	MXI1	chr2:47166976-47169461	HepG2	liver:	n/a	n/a
48	CTCF	chr2:47168880-47169030	HVMF	connective:	n/a	chr2:47168914-47168927
49	CTCF	chr2:47168800-47168950	MCF-7	breast:	n/a	chr2:47168914-47168927
50	TEAD4	chr2:47168665-47169125	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47167461..47169104-chr2:47203278..47205346,2	MCF-7	breast:
2	chr2:47166915..47170495-chr2:47399445..47404516,7	MCF-7	breast:
3	chr2:47166485..47169114-chr2:47402596..47405123,4	MCF-7	breast:
4	chr2:47139463..47143529-chr2:47167839..47169953,4	K562	blood:
5	chr2:47135393..47141252-chr2:47166022..47170880,5	K562	blood:
6	chr2:47168040..47171171-chr2:47402063..47404163,4	K562	blood:
7	chr2:47165446..47170208-chr2:47173646..47177856,9	MCF-7	breast:
8	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:
9	chr2:47167291..47170086-chr2:47204793..47207048,4	MCF-7	breast:
10	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
11	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:
12	chr2:47141557..47143529-chr2:47167839..47169788,2	K562	blood:
13	chr2:47141053..47143152-chr2:47167792..47169429,2	MCF-7	breast:
14	chr2:47166107..47171055-chr2:47402078..47404965,9	K562	blood:

Variant related genes	Relation type
MCFD2	TF binding region
ENSG00000272814	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10084332	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10164756	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10165085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10181411	0.85[AMR][1000 genomes]
rs10186980	0.85[AMR][1000 genomes]
rs11897050	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13391660	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13398748	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13406024	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13407588	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13409489	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13417753	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13424086	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13430346	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13430703	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17035878	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17035912	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28405928	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28465613	0.85[AMR][1000 genomes]
rs28529158	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28612371	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28770495	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4300885	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4314044	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4583513	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6729569	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73926967	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73926970	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73926978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73926980	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73926983	0.98[EUR][1000 genomes]
rs73926986	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73926988	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7577816	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7603884	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9973769	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv3427405	chr2:47166973-47169821	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv3332265	chr2:47167448-47169546	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6755386	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	chr2:47167400-47169000	Active TSS	Right Atrium	heart
2	chr2:47167400-47169200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr2:47167400-47169400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:47167400-47169600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr2:47167600-47169000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:47167600-47169000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr2:47167600-47169000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr2:47167600-47169000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:47167600-47169000	Active TSS	Psoas Muscle	Psoas
10	chr2:47167600-47169200	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr2:47167600-47169200	Active TSS	Brain Substantia Nigra	brain
12	chr2:47167600-47169400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:47167600-47169400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:47167600-47169600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:47167600-47169600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:47167600-47169600	Active TSS	Primary T cells from cord blood	blood
17	chr2:47167600-47169600	Active TSS	Right Ventricle	heart
18	chr2:47167600-47169800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr2:47167600-47169800	Active TSS	Fetal Kidney	kidney
20	chr2:47167600-47169800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:47167600-47170000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:47167600-47170400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:47167600-47170400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:47167600-47170400	Active TSS	Rectal Smooth Muscle	rectum
25	chr2:47167600-47170600	Active TSS	Thymus	Thymus
26	chr2:47167800-47169000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:47167800-47169000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:47167800-47169000	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr2:47167800-47169000	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr2:47167800-47169000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:47167800-47169000	Active TSS	Duodenum Mucosa	Duodenum
32	chr2:47167800-47169000	Active TSS	Fetal Intestine Large	intestine
33	chr2:47167800-47169000	Active TSS	Fetal Intestine Small	intestine
34	chr2:47167800-47169000	Active TSS	Fetal Lung	lung
35	chr2:47167800-47169000	Active TSS	HSMMtube	muscle
36	chr2:47167800-47169000	Active TSS	K562	blood
37	chr2:47167800-47169200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:47167800-47169200	Active TSS	Primary B cells from peripheral blood	blood
39	chr2:47167800-47169200	Active TSS	Brain Angular Gyrus	brain
40	chr2:47167800-47169200	Active TSS	Brain Anterior Caudate	brain
41	chr2:47167800-47169200	Active TSS	Brain Cingulate Gyrus	brain
42	chr2:47167800-47169200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:47167800-47169200	Active TSS	Colon Smooth Muscle	Colon
44	chr2:47167800-47169200	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr2:47167800-47169400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:47167800-47169400	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr2:47167800-47169400	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr2:47167800-47169400	Active TSS	Ovary	ovary
49	chr2:47167800-47169600	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr2:47167800-47169600	Active TSS	Lung	lung

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