Variant report

Variant	rs10012093
Chromosome Location	chr4:7047823-7047824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr4:7047648-7047982	GM12892	blood:	n/a	n/a
2	PAX5	chr4:7047625-7048020	GM12892	blood:	n/a	n/a
3	EBF1	chr4:7047621-7048123	GM12878	blood:	n/a	n/a
4	CTCF	chr4:7047818-7047825	GM12892	blood:	n/a	n/a
5	SMC3	chr4:7047596-7047987	GM12878	blood:	n/a	n/a
6	BHLHE40	chr4:7047584-7048161	GM12878	blood:	n/a	n/a
7	EP300	chr4:7047695-7047970	GM12878	blood:	n/a	n/a
8	EBF1	chr4:7047600-7048111	GM12878	blood:	n/a	n/a
9	PAX5	chr4:7047484-7048113	GM12878	blood:	n/a	n/a
10	EBF1	chr4:7047528-7048120	GM12878	blood:	n/a	n/a
11	BATF	chr4:7047609-7047848	GM12878	blood:	n/a	chr4:7047699-7047710
12	ATF2	chr4:7047504-7048039	GM12878	blood:	n/a	n/a
13	WRNIP1	chr4:7047501-7048105	GM12878	blood:	n/a	n/a
14	PAX5	chr4:7047655-7047979	GM12891	blood:	n/a	n/a
15	POLR2A	chr4:7047647-7047900	GM12878	blood:	n/a	n/a
16	MAX	chr4:7047677-7048016	GM12878	blood:	n/a	n/a
17	PAX5	chr4:7047763-7047932	GM12891	blood:	n/a	n/a
18	PAX5	chr4:7047699-7047996	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:7047365-7047954	K562	blood:	n/a	n/a
20	TBL1XR1	chr4:7047534-7047995	GM12878	blood:	n/a	n/a
21	RUNX3	chr4:7047436-7048077	GM12878	blood:	n/a	n/a
22	CTCF	chr4:7047720-7047870	RPTEC	kidney:	n/a	n/a
23	PAX5	chr4:7047592-7048077	GM12878	blood:	n/a	n/a
24	TCF3	chr4:7047594-7047959	GM12878	blood:	n/a	n/a
25	STAT3	chr4:7047750-7047949	MCF10A-Er-Src	breast:	n/a	n/a
26	RUNX3	chr4:7047411-7048125	GM12878	blood:	n/a	n/a
27	CTCF	chr4:7047761-7048082	GM12878	blood:	n/a	n/a
28	PAX5	chr4:7047602-7048123	GM12878	blood:	n/a	n/a
29	CTCF	chr4:7047680-7047830	GM12869	blood:	n/a	n/a
30	ESR1	chr4:7047613-7048015	T-47D	breast:	n/a	n/a
31	POLR2A	chr4:7047358-7047954	GM12878	blood:	n/a	n/a
32	CHD2	chr4:7047671-7047973	GM12878	blood:	n/a	n/a
33	MTA3	chr4:7047165-7048166	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7041999..7051916-chr4:7066728..7075643,37	MCF-7	breast:
2	chr4:7042421..7051559-chr4:7062214..7072674,24	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC96-1	chr4:7047386-7047958	ENSG00000245748

No data

Variant related genes	Relation type
CCDC96	TF binding region
ENSG00000109519	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10937781	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13113578	0.87[EUR][1000 genomes]
rs3951347	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4513569	0.87[EUR][1000 genomes]
rs4689062	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4689063	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4689582	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4689588	0.87[EUR][1000 genomes]
rs6814746	0.87[EUR][1000 genomes]
rs6832413	0.87[EUR][1000 genomes]
rs6841824	0.87[EUR][1000 genomes]
rs6849547	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7666504	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7673889	1.00[CEU][hapmap]
rs7699619	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs871133	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs907522	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs907524	0.87[EUR][1000 genomes]
rs907525	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9985704	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv469847	chr4:7003525-7168441	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv878531	chr4:7006541-7129556	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv878532	chr4:7010504-7055603	Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv878533	chr4:7032180-7063524	Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv4217	chr4:7035512-7080230	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	esv1801315	chr4:7044007-7052777	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv1835149	chr4:7044007-7052777	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv593556	chr4:7044447-7048842	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	esv1798014	chr4:7044504-7052182	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7045400-7048000	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr4:7045800-7048200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr4:7045800-7049400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr4:7046200-7048000	Enhancers	Placenta Amnion	Placenta Amnion
5	chr4:7046200-7048800	Flanking Active TSS	HSMM	muscle
6	chr4:7046200-7068600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:7046400-7048000	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr4:7046400-7048000	Flanking Active TSS	Rectal Smooth Muscle	rectum
9	chr4:7046400-7049000	Flanking Active TSS	GM12878-XiMat	blood
10	chr4:7046400-7049800	Enhancers	Primary B cells from peripheral blood	blood
11	chr4:7046400-7049800	Genic enhancers	Spleen	Spleen
12	chr4:7046600-7048000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr4:7046600-7048400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:7046600-7048600	Enhancers	Small Intestine	intestine
15	chr4:7046600-7049400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:7046600-7050400	Enhancers	Lung	lung
17	chr4:7046600-7050800	Genic enhancers	Fetal Muscle Leg	muscle
18	chr4:7046600-7051400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr4:7046600-7053800	Weak transcription	A549	lung
20	chr4:7046600-7055600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:7046600-7055600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:7046600-7055800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:7046600-7062600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:7046800-7048400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:7046800-7048800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:7046800-7048800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr4:7046800-7048800	Genic enhancers	Fetal Stomach	stomach
28	chr4:7046800-7049000	Enhancers	Fetal Thymus	thymus
29	chr4:7046800-7049200	Enhancers	HSMMtube	muscle
30	chr4:7046800-7049400	Enhancers	Liver	Liver
31	chr4:7046800-7049400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
32	chr4:7046800-7049800	Enhancers	Left Ventricle	heart
33	chr4:7046800-7050000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr4:7046800-7050000	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr4:7046800-7050000	Enhancers	Psoas Muscle	Psoas
36	chr4:7046800-7062000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:7047000-7048000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:7047000-7048000	Genic enhancers	HepG2	liver
39	chr4:7047000-7048000	Enhancers	HMEC	breast
40	chr4:7047000-7048200	Genic enhancers	Esophagus	oesophagus
41	chr4:7047000-7048400	Enhancers	Primary B cells from cord blood	blood
42	chr4:7047000-7048400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
43	chr4:7047000-7048400	Enhancers	Stomach Mucosa	stomach
44	chr4:7047000-7048600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:7047000-7048600	Enhancers	Fetal Brain Male	brain
46	chr4:7047000-7048600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr4:7047000-7048800	Enhancers	NHDF-Ad	bronchial
48	chr4:7047000-7049400	Enhancers	Colonic Mucosa	Colon
49	chr4:7047000-7049400	Enhancers	Ovary	ovary
50	chr4:7047000-7049400	Enhancers	Right Ventricle	heart

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