Variant report

Variant	rs13407588
Chromosome Location	chr2:47167133-47167134
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	ZNF263	chr2:47167047-47167629	K562	blood:	n/a	n/a
2	ZKSCAN1	chr2:47167086-47167487	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr2:47166976-47169461	HepG2	liver:	n/a	n/a
4	ZNF263	chr2:47167014-47167636	HEK293-T-REx	kidney:	n/a	n/a
5	POLR2A	chr2:47166646-47169549	HepG2	liver:	n/a	n/a
6	HEY1	chr2:47167080-47169431	HepG2	liver:	n/a	chr2:47167527-47167542
7	MAX	chr2:47166482-47169616	HepG2	liver:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47166847-47166856 chr2:47167751-47167760
8	MXI1	chr2:47167052-47169691	SK-N-SH	brain:	n/a	n/a
9	TFAP2A	chr2:47166511-47169094	Hela-S3	cervix:	n/a	chr2:47166818-47166829 chr2:47166818-47166829 chr2:47166814-47166829 chr2:47166818-47166829 chr2:47166818-47166829
10	POLR2A	chr2:47166996-47167201	HUVEC	blood vessel:	n/a	n/a
11	TCF7L2	chr2:47166677-47168133	Hela-S3	cervix:	n/a	chr2:47166924-47166934 chr2:47166926-47166935
12	MAX	chr2:47167034-47169701	A549	lung:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
13	POLR2A	chr2:47166646-47169518	Hela-S3	cervix:	n/a	n/a
14	MAZ	chr2:47166483-47170044	IMR90	lung:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47166847-47166856 chr2:47167751-47167760
15	RCOR1	chr2:47166789-47168450	Hela-S3	cervix:	n/a	n/a
16	MAX	chr2:47166973-47170077	A549	lung:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
17	TCF12	chr2:47166525-47169821	A549	lung:	n/a	chr2:47168022-47168032 chr2:47166841-47166849
18	MXI1	chr2:47166913-47169815	IMR90	lung:	n/a	n/a
19	TFAP2C	chr2:47166619-47169130	Hela-S3	cervix:	n/a	chr2:47166814-47166829
20	MYBL2	chr2:47166822-47167893	HepG2	liver:	n/a	n/a
21	SMARCC1	chr2:47166624-47167989	Hela-S3	cervix:	n/a	n/a
22	NFIC	chr2:47167130-47167844	HepG2	liver:	n/a	chr2:47167468-47167496
23	POLR2A	chr2:47166628-47169589	HepG2	liver:	n/a	n/a
24	MBD4	chr2:47166896-47168133	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:47167114-47169742	Hela-S3	cervix:	n/a	n/a
26	MAZ	chr2:47166890-47167334	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47166662..47168239-chr2:47214409..47216366,2	MCF-7	breast:
2	chr2:47166915..47170495-chr2:47399445..47404516,7	MCF-7	breast:
3	chr2:47166648..47168601-chr2:47272959..47275479,2	MCF-7	breast:
4	chr2:47166510..47168193-chr2:47197498..47199709,2	MCF-7	breast:
5	chr2:47166485..47169114-chr2:47402596..47405123,4	MCF-7	breast:
6	chr2:46768715..46770395-chr2:47165746..47168568,2	MCF-7	breast:
7	chr2:47135393..47141252-chr2:47166022..47170880,5	K562	blood:
8	chr2:47165446..47170208-chr2:47173646..47177856,9	MCF-7	breast:
9	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:
10	chr2:47126017..47127666-chr2:47165711..47167626,2	MCF-7	breast:
11	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
12	chr2:47166107..47171055-chr2:47402078..47404965,9	K562	blood:

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000250565	Chromatin interaction
ENSG00000228925	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10084332	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10164756	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10165085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10181411	0.85[AMR][1000 genomes]
rs10186980	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11897050	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13391660	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13398748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13406024	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13409489	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13417753	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13424086	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13430346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13430703	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17035878	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17035912	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28405928	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28465613	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28529158	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28612371	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28770495	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4300885	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4314044	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4583513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6729569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6755386	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73926967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926979	0.82[AFR][1000 genomes]
rs73926980	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926983	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73926986	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926988	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7577816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7603884	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9973769	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13407588	MCFD2	cis	Artery Tibial	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47146000-47167400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:47160000-47167200	Weak transcription	Fetal Stomach	stomach
3	chr2:47166200-47167200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr2:47166200-47167400	Enhancers	Placenta	Placenta
5	chr2:47166400-47167200	Enhancers	Stomach Smooth Muscle	stomach
6	chr2:47166400-47167400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:47166400-47167400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:47166400-47167400	Enhancers	Primary B cells from peripheral blood	blood
9	chr2:47166400-47167600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:47166400-47167600	Enhancers	Dnd41	blood
11	chr2:47166400-47167800	Flanking Active TSS	Hela-S3	cervix
12	chr2:47166600-47167200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:47166600-47167200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:47166600-47167200	Enhancers	Primary hematopoietic stem cells	blood
15	chr2:47166600-47167200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:47166600-47167200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:47166600-47167200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:47166600-47167200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:47166600-47167200	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr2:47166600-47167200	Enhancers	HMEC	breast
21	chr2:47166600-47167200	Enhancers	NHEK	skin
22	chr2:47166600-47167200	Enhancers	NHLF	lung
23	chr2:47166600-47167400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:47166600-47167400	Enhancers	Fetal Intestine Large	intestine
25	chr2:47166600-47167400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:47166600-47167600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:47166600-47167600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:47166600-47167600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:47166600-47167600	Enhancers	Fetal Intestine Small	intestine
30	chr2:47166600-47167600	Enhancers	Right Ventricle	heart
31	chr2:47166600-47167600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr2:47166600-47167600	Enhancers	Stomach Mucosa	stomach
33	chr2:47166600-47167800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:47166600-47167800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:47166600-47167800	Enhancers	Left Ventricle	heart
36	chr2:47166600-47167800	Enhancers	Lung	lung
37	chr2:47166600-47167800	Enhancers	Pancreas	Pancrea
38	chr2:47166600-47167800	Enhancers	Placenta Amnion	Placenta Amnion
39	chr2:47166600-47167800	Enhancers	Spleen	Spleen
40	chr2:47166600-47168000	Enhancers	Fetal Heart	heart
41	chr2:47166800-47167200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
42	chr2:47166800-47167200	Enhancers	Primary T cells from cord blood	blood
43	chr2:47166800-47167200	Enhancers	Adipose Nuclei	Adipose
44	chr2:47166800-47167200	Enhancers	Colon Smooth Muscle	Colon
45	chr2:47166800-47167200	Flanking Active TSS	HepG2	liver
46	chr2:47166800-47167200	Enhancers	K562	blood
47	chr2:47166800-47167400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr2:47166800-47167400	Enhancers	Fetal Muscle Trunk	muscle
49	chr2:47166800-47167400	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr2:47166800-47167400	Enhancers	NH-A	brain

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