Variant report

Variant	rs56213467
Chromosome Location	chr2:47165608-47165609
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:47165560-47165710	AG09319	gingival:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47164600..47167090-chr2:47190950..47193614,2	K562	blood:
2	chr2:47165446..47170208-chr2:47173646..47177856,9	MCF-7	breast:
3	chr2:47163957..47166011-chr2:47167875..47170723,3	K562	blood:
4	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
5	chr2:47152234..47154718-chr2:47163994..47166479,3	MCF-7	breast:
6	chr2:47142704..47145224-chr2:47163492..47166799,3	K562	blood:

No data

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10174894	0.92[ASN][1000 genomes]
rs10190862	0.94[EUR][1000 genomes]
rs10190882	0.94[EUR][1000 genomes]
rs10197474	0.94[EUR][1000 genomes]
rs10199965	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11890177	0.91[ASN][1000 genomes]
rs11894319	0.92[ASN][1000 genomes]
rs13388612	0.96[ASN][1000 genomes]
rs13392448	0.94[ASN][1000 genomes]
rs13394007	0.94[EUR][1000 genomes]
rs13398851	0.83[ASN][1000 genomes]
rs13410702	0.94[EUR][1000 genomes]
rs13415655	0.94[EUR][1000 genomes]
rs13415771	0.94[EUR][1000 genomes]
rs13419072	0.94[EUR][1000 genomes]
rs1446499	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1446500	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17035859	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17035867	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17035884	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17035887	0.91[ASN][1000 genomes]
rs2084192	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289927	0.92[ASN][1000 genomes]
rs2289928	0.92[ASN][1000 genomes]
rs2347259	0.85[ASN][1000 genomes]
rs28516550	0.91[ASN][1000 genomes]
rs3087857	0.96[ASN][1000 genomes]
rs34581142	0.92[ASN][1000 genomes]
rs35433380	0.92[ASN][1000 genomes]
rs55872217	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58589709	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60194846	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61132855	0.85[ASN][1000 genomes]
rs62136788	0.94[EUR][1000 genomes]
rs62136818	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62136819	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62136820	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136822	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62136823	0.92[ASN][1000 genomes]
rs62136825	0.92[ASN][1000 genomes]
rs62136827	0.92[ASN][1000 genomes]
rs62140550	0.96[ASN][1000 genomes]
rs62140553	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62140556	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6544938	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544939	0.94[ASN][1000 genomes]
rs6706031	0.92[ASN][1000 genomes]
rs6715391	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6715620	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6716381	0.96[ASN][1000 genomes]
rs6722440	0.92[ASN][1000 genomes]
rs6729120	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6729604	0.96[ASN][1000 genomes]
rs6733548	0.96[ASN][1000 genomes]
rs6743966	0.91[ASN][1000 genomes]
rs6743994	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6745578	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6755303	0.98[ASN][1000 genomes]
rs6758093	0.96[ASN][1000 genomes]
rs6758512	0.92[ASN][1000 genomes]
rs71423929	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs720827	0.94[EUR][1000 genomes]
rs7340475	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73926966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs754411	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7565420	0.87[ASN][1000 genomes]
rs7574514	0.81[ASN][1000 genomes]
rs7575172	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7586004	0.91[ASN][1000 genomes]
rs7596198	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7601491	0.96[ASN][1000 genomes]
rs8861	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9973504	0.94[ASN][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
rs56213467	MCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47144200-47166600	Weak transcription	Pancreas	Pancrea
2	chr2:47144800-47167000	Weak transcription	Fetal Lung	lung
3	chr2:47146000-47167400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:47150600-47166600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:47150600-47167000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:47151000-47166800	Weak transcription	Small Intestine	intestine
7	chr2:47153800-47166600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:47154000-47166400	Weak transcription	Hela-S3	cervix
9	chr2:47154400-47166800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:47155800-47166600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:47157200-47166600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:47157400-47166600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:47160000-47167200	Weak transcription	Fetal Stomach	stomach
14	chr2:47160600-47166800	Weak transcription	GM12878-XiMat	blood
15	chr2:47161600-47166600	Weak transcription	Primary B cells from cord blood	blood
16	chr2:47161600-47166600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:47161600-47166600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:47161600-47166800	Weak transcription	Primary T cells from cord blood	blood
19	chr2:47162400-47166800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:47163800-47166400	Weak transcription	Osteobl	bone
21	chr2:47164000-47166600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:47164400-47166800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:47164800-47166000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr2:47165000-47166400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:47165000-47166400	Weak transcription	Fetal Thymus	thymus
26	chr2:47165000-47166400	Weak transcription	Thymus	Thymus
27	chr2:47165000-47166400	Weak transcription	HepG2	liver
28	chr2:47165000-47166600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:47165000-47166600	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:47165000-47166600	Weak transcription	Spleen	Spleen
31	chr2:47165200-47166400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:47165200-47166400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:47165200-47166400	Weak transcription	A549	lung
34	chr2:47165200-47166400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr2:47165400-47166400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr2:47165400-47167000	Weak transcription	Right Atrium	heart

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