Variant report

Variant	rs6729120
Chromosome Location	chr2:47144629-47144630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

(count:6 , 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	NFIC	chr2:47144615-47145172	GM12878	blood:	n/a	n/a
3	NFIC	chr2:47144619-47145186	GM12878	blood:	n/a	n/a
4	MTA3	chr2:47144629-47145178	GM12878	blood:	n/a	n/a
5	POU2F2	chr2:47144586-47145194	GM12878	blood:	n/a	n/a
6	RUNX3	chr2:47144581-47145207	GM12878	blood:	n/a	n/a

No data

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

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

No data

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

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10174894	0.96[ASN][1000 genomes]
rs10190862	0.94[EUR][1000 genomes]
rs10190882	0.94[EUR][1000 genomes]
rs10197474	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10199965	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs11890177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11894319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13388612	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13392448	0.94[ASN][1000 genomes]
rs13394007	0.94[EUR][1000 genomes]
rs13398851	0.87[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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1446500	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17035813	1.00[CEU][hapmap]
rs17035859	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17035867	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17035884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17035887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17036060	0.88[CHB][hapmap]
rs2084192	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289927	0.96[ASN][1000 genomes]
rs2289928	0.96[ASN][1000 genomes]
rs2347259	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs28516550	0.94[ASN][1000 genomes]
rs3087857	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34581142	0.96[ASN][1000 genomes]
rs35433380	0.96[ASN][1000 genomes]
rs4505575	0.81[ASN][1000 genomes]
rs55872217	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56213467	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58589709	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60194846	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61132855	0.88[ASN][1000 genomes]
rs62136788	0.94[EUR][1000 genomes]
rs62136818	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136819	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136820	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62136822	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136823	0.96[ASN][1000 genomes]
rs62136825	0.96[ASN][1000 genomes]
rs62136827	0.96[ASN][1000 genomes]
rs62140550	1.00[ASN][1000 genomes]
rs62140553	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62140556	0.85[AMR][1000 genomes]
rs6544938	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544939	0.98[ASN][1000 genomes]
rs6706031	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6715391	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715620	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716381	1.00[ASN][1000 genomes]
rs6722440	0.96[ASN][1000 genomes]
rs6729604	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6733548	1.00[ASN][1000 genomes]
rs6743966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6743994	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745578	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6755303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6758093	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[ASN][1000 genomes]
rs6758512	0.96[ASN][1000 genomes]
rs71423929	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720827	0.94[EUR][1000 genomes]
rs7340475	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73926966	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754411	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7565420	0.90[ASN][1000 genomes]
rs7574514	0.89[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7574833	0.88[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7575172	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[ASN][1000 genomes]
rs7596198	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601491	1.00[ASN][1000 genomes]
rs8861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9973504	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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47142200-47144800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr2:47143400-47145400	Flanking Active TSS	Dnd41	blood
3	chr2:47143800-47145200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:47143800-47146000	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr2:47143800-47146000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:47143800-47146000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:47143800-47146000	Weak transcription	Stomach Mucosa	stomach
8	chr2:47143800-47146200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:47143800-47146200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:47143800-47146200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:47143800-47146400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:47143800-47147200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:47143800-47147200	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:47143800-47148800	Weak transcription	NH-A	brain
15	chr2:47143800-47149000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:47143800-47151800	Weak transcription	Lung	lung
17	chr2:47144000-47144800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr2:47144000-47144800	Enhancers	Small Intestine	intestine
19	chr2:47144000-47145000	Enhancers	Adipose Nuclei	Adipose
20	chr2:47144000-47145000	Enhancers	Liver	Liver
21	chr2:47144000-47145000	Flanking Active TSS	K562	blood
22	chr2:47144000-47146000	Flanking Active TSS	GM12878-XiMat	blood
23	chr2:47144000-47146200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr2:47144000-47146200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr2:47144000-47146200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr2:47144000-47148800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:47144000-47150800	Weak transcription	Placenta	Placenta
28	chr2:47144200-47144800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr2:47144200-47144800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:47144200-47144800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:47144200-47144800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:47144200-47144800	Enhancers	Brain Angular Gyrus	brain
33	chr2:47144200-47144800	Enhancers	Fetal Lung	lung
34	chr2:47144200-47144800	Enhancers	NHEK	skin
35	chr2:47144200-47145000	Enhancers	Colon Smooth Muscle	Colon
36	chr2:47144200-47145000	Enhancers	Fetal Brain Female	brain
37	chr2:47144200-47145200	Enhancers	Brain Anterior Caudate	brain
38	chr2:47144200-47145400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:47144200-47145800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr2:47144200-47145800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:47144200-47146000	Enhancers	Duodenum Mucosa	Duodenum
42	chr2:47144200-47146200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:47144200-47146600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:47144200-47148400	Weak transcription	HUVEC	blood vessel
45	chr2:47144200-47149200	Weak transcription	NHDF-Ad	bronchial
46	chr2:47144200-47149800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:47144200-47150000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:47144200-47150200	Weak transcription	Gastric	stomach
49	chr2:47144200-47151800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr2:47144200-47153000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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