Variant report

Variant	rs13430346
Chromosome Location	chr2:47166822-47166823
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	NR2F2	chr2:47166541-47167047	MCF-7	breast:	n/a	n/a
2	MAZ	chr2:47166757-47167066	Hela-S3	cervix:	n/a	chr2:47166847-47166856
3	NR3C1	chr2:47166580-47167118	A549	lung:	n/a	chr2:47166853-47166879 chr2:47166853-47166879 chr2:47166853-47166879
4	NR3C1	chr2:47166631-47167037	A549	lung:	n/a	chr2:47166853-47166879 chr2:47166853-47166879 chr2:47166853-47166879
5	POLR2A	chr2:47166646-47169549	HepG2	liver:	n/a	n/a
6	SMC3	chr2:47166726-47167027	Hela-S3	cervix:	n/a	n/a
7	ZNF217	chr2:47166749-47166965	MCF-7	breast:	n/a	n/a
8	NR3C1	chr2:47166525-47167081	A549	lung:	n/a	chr2:47166853-47166879 chr2:47166853-47166879 chr2:47166853-47166879
9	RFX5	chr2:47166742-47167014	Hela-S3	cervix:	n/a	n/a
10	MAX	chr2:47166482-47169616	HepG2	liver:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47166847-47166856 chr2:47167751-47167760
11	NR3C1	chr2:47166706-47166988	A549	lung:	n/a	chr2:47166853-47166879 chr2:47166853-47166879 chr2:47166853-47166879
12	TFAP2A	chr2:47166511-47169094	Hela-S3	cervix:	n/a	chr2:47166818-47166829 chr2:47166818-47166829 chr2:47166814-47166829 chr2:47166818-47166829 chr2:47166818-47166829
13	ELK1	chr2:47166777-47166940	Hela-S3	cervix:	n/a	n/a
14	TCF7L2	chr2:47166677-47168133	Hela-S3	cervix:	n/a	chr2:47166924-47166934 chr2:47166926-47166935
15	POLR2A	chr2:47166646-47169518	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr2:47166483-47170044	IMR90	lung:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47166847-47166856 chr2:47167751-47167760
17	RCOR1	chr2:47166789-47168450	Hela-S3	cervix:	n/a	n/a
18	TCF12	chr2:47166525-47169821	A549	lung:	n/a	chr2:47168022-47168032 chr2:47166841-47166849
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	POLR2A	chr2:47166628-47169589	HepG2	liver:	n/a	n/a
23	MAX	chr2:47166760-47166935	Hela-S3	cervix:	n/a	chr2:47166847-47166856

No.	Distal block	Cell Line	Cell type
1	chr2:47166662..47168239-chr2:47214409..47216366,2	MCF-7	breast:
2	chr2:47164600..47167090-chr2:47190950..47193614,2	K562	blood:
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	chr2:47126017..47127666-chr2:47165711..47167626,2	MCF-7	breast:
10	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
11	chr2:47166107..47171055-chr2:47402078..47404965,9	K562	blood:

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

Extended variants
information (count: 42 )
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]
rs13407588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13430346	MCFD2	cis	Artery Tibial	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47144800-47167000	Weak transcription	Fetal Lung	lung
2	chr2:47146000-47167400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:47150600-47167000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:47160000-47167200	Weak transcription	Fetal Stomach	stomach
5	chr2:47165400-47167000	Weak transcription	Right Atrium	heart
6	chr2:47166200-47167200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr2:47166200-47167400	Enhancers	Placenta	Placenta
8	chr2:47166400-47167000	Enhancers	Duodenum Mucosa	Duodenum
9	chr2:47166400-47167000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr2:47166400-47167000	Enhancers	Osteobl	bone
11	chr2:47166400-47167200	Enhancers	Stomach Smooth Muscle	stomach
12	chr2:47166400-47167400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:47166400-47167400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr2:47166400-47167400	Enhancers	Primary B cells from peripheral blood	blood
15	chr2:47166400-47167600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:47166400-47167600	Enhancers	Dnd41	blood
17	chr2:47166400-47167800	Flanking Active TSS	Hela-S3	cervix
18	chr2:47166600-47167000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr2:47166600-47167000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr2:47166600-47167000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:47166600-47167000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:47166600-47167000	Enhancers	Primary B cells from cord blood	blood
23	chr2:47166600-47167000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:47166600-47167000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:47166600-47167000	Enhancers	Brain Hippocampus Middle	brain
26	chr2:47166600-47167000	Enhancers	HSMMtube	muscle
27	chr2:47166600-47167000	Enhancers	NHDF-Ad	bronchial
28	chr2:47166600-47167200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:47166600-47167200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:47166600-47167200	Enhancers	Primary hematopoietic stem cells	blood
31	chr2:47166600-47167200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:47166600-47167200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:47166600-47167200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:47166600-47167200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:47166600-47167200	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr2:47166600-47167200	Enhancers	HMEC	breast
37	chr2:47166600-47167200	Enhancers	NHEK	skin
38	chr2:47166600-47167200	Enhancers	NHLF	lung
39	chr2:47166600-47167400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:47166600-47167400	Enhancers	Fetal Intestine Large	intestine
41	chr2:47166600-47167400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr2:47166600-47167600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:47166600-47167600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:47166600-47167600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:47166600-47167600	Enhancers	Fetal Intestine Small	intestine
46	chr2:47166600-47167600	Enhancers	Right Ventricle	heart
47	chr2:47166600-47167600	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr2:47166600-47167600	Enhancers	Stomach Mucosa	stomach
49	chr2:47166600-47167800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:47166600-47167800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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