Variant report

Variant	rs6729604
Chromosome Location	chr2:47145002-47145003
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr2:47144621-47145162	GM12878	blood:	n/a	n/a
2	ZNF143	chr2:47144835-47145035	GM12878	blood:	n/a	n/a
3	NFIC	chr2:47144615-47145172	GM12878	blood:	n/a	n/a
4	BCLAF1	chr2:47144656-47145128	GM12878	blood:	n/a	n/a
5	EP300	chr2:47144801-47145041	K562	blood:	n/a	n/a
6	NFIC	chr2:47144619-47145186	GM12878	blood:	n/a	n/a
7	TAL1	chr2:47144692-47145109	K562	blood:	n/a	n/a
8	POU2F2	chr2:47144733-47145062	GM12891	blood:	n/a	n/a
9	ARID3A	chr2:47144904-47145130	K562	blood:	n/a	n/a
10	POU2F2	chr2:47144653-47145111	GM12878	blood:	n/a	n/a
11	RCOR1	chr2:47144800-47145295	GM12878	blood:	n/a	n/a
12	IRF4	chr2:47144677-47145195	GM12878	blood:	n/a	n/a
13	BHLHE40	chr2:47144739-47145441	GM12878	blood:	n/a	n/a
14	MTA3	chr2:47144629-47145178	GM12878	blood:	n/a	n/a
15	TBL1XR1	chr2:47144707-47145202	GM12878	blood:	n/a	n/a
16	SP1	chr2:47144643-47145206	GM12878	blood:	n/a	n/a
17	POU2F2	chr2:47144675-47145061	GM12891	blood:	n/a	n/a
18	TBP	chr2:47144735-47145258	GM12878	blood:	n/a	n/a
19	SP1	chr2:47144641-47145078	GM12878	blood:	n/a	n/a
20	PAX5	chr2:47144640-47145187	GM12878	blood:	n/a	n/a
21	IRF4	chr2:47144700-47145150	GM12878	blood:	n/a	n/a
22	EP300	chr2:47144763-47145215	GM12878	blood:	n/a	n/a
23	EP300	chr2:47144745-47145246	GM12878	blood:	n/a	n/a
24	EBF1	chr2:47144732-47145077	GM12878	blood:	n/a	n/a
25	BATF	chr2:47144682-47145267	GM12878	blood:	n/a	n/a
26	EBF1	chr2:47144793-47145054	GM12878	blood:	n/a	n/a
27	POU2F2	chr2:47144586-47145194	GM12878	blood:	n/a	n/a
28	BCL11A	chr2:47144767-47145166	GM12878	blood:	n/a	n/a
29	POU2F2	chr2:47144741-47145003	GM12878	blood:	n/a	n/a
30	BATF	chr2:47144679-47145276	GM12878	blood:	n/a	n/a
31	RUNX3	chr2:47144581-47145207	GM12878	blood:	n/a	n/a
32	RUNX3	chr2:47144643-47145294	GM12878	blood:	n/a	n/a
33	BCL11A	chr2:47144692-47145250	GM12878	blood:	n/a	n/a
34	FOXM1	chr2:47144722-47145113	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47142780..47146808-chr2:47401206..47405117,7	K562	blood:
2	chr2:47144874..47146939-chr2:47165957..47169757,3	K562	blood:
3	chr2:47140335..47142832-chr2:47143395..47145229,2	K562	blood:
4	chr2:47140743..47148534-chr2:47401019..47406419,10	MCF-7	breast:
5	chr2:47144648..47146323-chr2:47215712..47217737,2	MCF-7	breast:
6	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
7	chr2:47143555..47145098-chr2:47147081..47148697,2	K562	blood:
8	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:

No data

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

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10168851	0.85[EUR][1000 genomes]
rs10174894	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10199965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11890177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11894319	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]
rs13388612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392448	0.94[ASN][1000 genomes]
rs13398851	0.87[ASN][1000 genomes]
rs13423962	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13432713	0.80[EUR][1000 genomes]
rs1446499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1446500	1.00[ASN][1000 genomes]
rs17035859	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs17035867	0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
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];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17036060	0.88[CHB][hapmap]
rs2084192	1.00[ASN][1000 genomes]
rs2289927	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289928	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347259	0.88[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs28516550	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087857	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34581142	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs35433380	0.96[ASN][1000 genomes]
rs4505575	0.81[ASN][1000 genomes]
rs55872217	0.96[ASN][1000 genomes]
rs56213467	0.96[ASN][1000 genomes]
rs58589709	0.94[ASN][1000 genomes]
rs60194846	1.00[ASN][1000 genomes]
rs61132855	0.88[ASN][1000 genomes]
rs62136818	0.85[ASN][1000 genomes]
rs62136819	0.85[ASN][1000 genomes]
rs62136820	0.88[ASN][1000 genomes]
rs62136822	0.94[ASN][1000 genomes]
rs62136823	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62136825	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62136827	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62140550	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62140553	0.84[ASN][1000 genomes]
rs6544938	0.98[ASN][1000 genomes]
rs6544939	0.98[ASN][1000 genomes]
rs6706031	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6715391	0.94[ASN][1000 genomes]
rs6715620	1.00[ASN][1000 genomes]
rs6716381	1.00[ASN][1000 genomes]
rs6722440	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6729120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6733548	1.00[ASN][1000 genomes]
rs6743966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6743994	0.94[ASN][1000 genomes]
rs6745578	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6755303	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[ASN][1000 genomes]
rs6758093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758512	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71423929	1.00[ASN][1000 genomes]
rs7340475	0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs73926966	1.00[ASN][1000 genomes]
rs754411	0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7565420	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7574514	0.89[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7574833	0.88[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7575172	1.00[ASN][1000 genomes]
rs7586004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7596198	0.94[ASN][1000 genomes]
rs7601491	1.00[ASN][1000 genomes]
rs8861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9973504	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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
rs6729604	MCFD2	cis	Artery Tibial	GTEx
rs6729604	MCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47143400-47145400	Flanking Active TSS	Dnd41	blood
2	chr2:47143800-47145200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:47143800-47146000	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr2:47143800-47146000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:47143800-47146000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:47143800-47146000	Weak transcription	Stomach Mucosa	stomach
7	chr2:47143800-47146200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:47143800-47146200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:47143800-47146200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr2:47143800-47146400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:47143800-47147200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:47143800-47147200	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:47143800-47148800	Weak transcription	NH-A	brain
14	chr2:47143800-47149000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:47143800-47151800	Weak transcription	Lung	lung
16	chr2:47144000-47146000	Flanking Active TSS	GM12878-XiMat	blood
17	chr2:47144000-47146200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:47144000-47146200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:47144000-47146200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr2:47144000-47148800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:47144000-47150800	Weak transcription	Placenta	Placenta
22	chr2:47144200-47145200	Enhancers	Brain Anterior Caudate	brain
23	chr2:47144200-47145400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:47144200-47145800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:47144200-47145800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:47144200-47146000	Enhancers	Duodenum Mucosa	Duodenum
27	chr2:47144200-47146200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:47144200-47146600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:47144200-47148400	Weak transcription	HUVEC	blood vessel
30	chr2:47144200-47149200	Weak transcription	NHDF-Ad	bronchial
31	chr2:47144200-47149800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:47144200-47150000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:47144200-47150200	Weak transcription	Gastric	stomach
34	chr2:47144200-47151800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:47144200-47153000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:47144200-47153200	Weak transcription	Fetal Stomach	stomach
37	chr2:47144200-47153800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:47144200-47154000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:47144200-47155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:47144200-47157200	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:47144200-47166600	Weak transcription	Pancreas	Pancrea
42	chr2:47144400-47145200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:47144400-47145200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:47144400-47145200	Enhancers	Hela-S3	cervix
45	chr2:47144400-47145200	Weak transcription	NHLF	lung
46	chr2:47144400-47145600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:47144400-47146000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:47144400-47146800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:47144400-47146800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:47144400-47147000	Enhancers	Primary B cells from cord blood	blood

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