Variant report

Variant	rs3181228
Chromosome Location	chr6:24667662-24667663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:239)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:239 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZKSCAN1	chr6:24666589-24667780	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:24666556-24667668	HCT-116	colon:	n/a	n/a
3	STAT3	chr6:24667117-24667666	MCF10A-Er-Src	breast:	n/a	chr6:24667613-24667624
4	HEY1	chr6:24666556-24668167	K562	blood:	n/a	chr6:24667242-24667257 chr6:24667220-24667235
5	HEY1	chr6:24666602-24667815	K562	blood:	n/a	chr6:24667242-24667257 chr6:24667220-24667235
6	RELA	chr6:24666637-24667859	GM19193	blood:	n/a	n/a
7	POLR2A	chr6:24666413-24667665	K562	blood:	n/a	n/a
8	SP1	chr6:24666870-24667714	H1-hESC	embryonic stem cell:	n/a	n/a
9	MXI1	chr6:24666632-24667865	GM12878	blood:	n/a	n/a
10	HEY1	chr6:24666386-24668037	HepG2	liver:	n/a	chr6:24667242-24667257 chr6:24667220-24667235
11	POLR2A	chr6:24666409-24667917	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT5A	chr6:24666771-24667663	K562	blood:	n/a	chr6:24667613-24667624
13	POLR2A	chr6:24666616-24667999	HepG2	liver:	n/a	n/a
14	JUN	chr6:24667341-24667921	HepG2	liver:	n/a	n/a
15	CEBPB	chr6:24667006-24667954	HepG2	liver:	n/a	n/a
16	CEBPB	chr6:24666530-24668034	Hela-S3	cervix:	n/a	n/a
17	MYC	chr6:24667116-24667679	HepG2	liver:	n/a	n/a
18	MAX	chr6:24666433-24667689	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr6:24666437-24667682	GM12892	blood:	n/a	n/a
20	MAZ	chr6:24666496-24667919	K562	blood:	n/a	n/a
21	RELA	chr6:24666508-24667955	GM10847	blood:	n/a	n/a
22	POLR2A	chr6:24666843-24668068	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr6:24666432-24668102	Hela-S3	cervix:	n/a	n/a
24	CEBPB	chr6:24667159-24667668	A549	lung:	n/a	n/a
25	NFIC	chr6:24666671-24668091	HepG2	liver:	n/a	n/a
26	UBTF	chr6:24666205-24668049	K562	blood:	n/a	n/a
27	POLR2A	chr6:24666311-24667878	PBDE	blood:	n/a	n/a
28	EP300	chr6:24666897-24667944	GM12878	blood:	n/a	chr6:24667160-24667167
29	STAT3	chr6:24667117-24667878	MCF10A-Er-Src	breast:	n/a	chr6:24667613-24667624
30	POLR2A	chr6:24666690-24667662	GM12892	blood:	n/a	n/a
31	SIN3A	chr6:24666296-24667709	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr6:24666539-24667712	ECC-1	luminal epithelium:	n/a	n/a
33	EP300	chr6:24666782-24668069	HepG2	liver:	n/a	chr6:24667160-24667167
34	TAF1	chr6:24666688-24667675	ECC-1	luminal epithelium:	n/a	n/a
35	HNF4A	chr6:24667000-24668081	HepG2	liver:	n/a	chr6:24667643-24667655 chr6:24667425-24667433 chr6:24667395-24667403 chr6:24667426-24667434
36	MTA3	chr6:24666606-24667989	GM12878	blood:	n/a	n/a
37	TBP	chr6:24666475-24667683	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr6:24666426-24667718	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr6:24666454-24668221	K562	blood:	n/a	n/a
40	STAT3	chr6:24667332-24668015	GM12878	blood:	n/a	chr6:24667613-24667624
41	CTCF	chr6:24667540-24667690	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:24666419-24668167	K562	blood:	n/a	n/a
43	POLR2A	chr6:24666496-24667988	HepG2	liver:	n/a	n/a
44	GTF2F1	chr6:24666551-24667706	K562	blood:	n/a	n/a
45	MYC	chr6:24666628-24668050	K562	blood:	n/a	n/a
46	MYBL2	chr6:24666374-24668048	HepG2	liver:	n/a	n/a
47	REST	chr6:24667377-24667670	SK-N-SH	brain:	n/a	n/a
48	ATF1	chr6:24666842-24667807	K562	blood:	n/a	n/a
49	FOSL2	chr6:24666807-24667664	HepG2	liver:	n/a	n/a
50	MAX	chr6:24666619-24667884	HepG2	liver:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24523688..24526663-chr6:24667463..24669411,2	K562	blood:
2	chr18:657846..658502-chr6:24667183..24667956,2	Hela-S3	cervix:
3	chr6:24666490..24670247-chr6:24774150..24780460,9	K562	blood:
4	chr6:24645863..24648986-chr6:24665821..24668897,5	MCF-7	breast:
5	chr6:24665480..24670247-chr6:24773496..24779775,9	K562	blood:
6	chr6:24666041..24667769-chr6:24719597..24721263,2	MCF-7	breast:
7	chr6:24494650..24496587-chr6:24665440..24668079,2	MCF-7	breast:
8	chr6:24494081..24496615-chr6:24665704..24668263,2	K562	blood:
9	chr6:24660920..24672880-chr6:24713381..24723000,42	K562	blood:
10	chr17:37844103..37844930-chr6:24666942..24667764,2	Hela-S3	cervix:
11	chr6:24665745..24668755-chr6:24718443..24722281,4	MCF-7	breast:
12	chr6:24620860..24623023-chr6:24667310..24669178,2	K562	blood:
13	chr6:24661385..24670379-chr6:24713871..24722680,32	K562	blood:
14	chr12:54674431..54674941-chr6:24667294..24667837,2	Hela-S3	cervix:
15	chr6:24645218..24647641-chr6:24665331..24668427,5	MCF-7	breast:

No data

Variant related genes	Relation type
TDP2	TF binding region
ENSG00000112312	Chromatin interaction
ENSG00000161395	Chromatin interaction
ENSG00000176890	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000141736	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000137261	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000176912	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11753290	0.83[CEU][hapmap]
rs17249505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883593	0.82[CHB][hapmap]
rs1923187	0.87[CEU][hapmap]
rs4544900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344861	0.81[EUR][1000 genomes]
rs6909099	0.83[EUR][1000 genomes]
rs6917209	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927947	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6928668	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931809	0.82[EUR][1000 genomes]
rs6937327	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937533	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757919	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7765904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356943	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9358791	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358793	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366577	0.82[CHB][hapmap]
rs9366580	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379685	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24664000-24668600	Active TSS	Colonic Mucosa	Colon
2	chr6:24664400-24668000	Active TSS	Fetal Intestine Large	intestine
3	chr6:24664600-24668000	Active TSS	Fetal Intestine Small	intestine
4	chr6:24665400-24668000	Active TSS	Sigmoid Colon	Sigmoid Colon
5	chr6:24665400-24668200	Active TSS	Psoas Muscle	Psoas
6	chr6:24665400-24668200	Active TSS	NHDF-Ad	bronchial
7	chr6:24665600-24667800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:24665600-24668000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:24665600-24668000	Active TSS	GM12878-XiMat	blood
10	chr6:24665600-24668200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:24665600-24668200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:24665600-24668200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:24665600-24668400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr6:24665600-24668400	Active TSS	NHLF	lung
15	chr6:24665800-24667800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:24665800-24667800	Active TSS	Stomach Smooth Muscle	stomach
17	chr6:24665800-24668000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:24665800-24668200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:24665800-24668200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:24665800-24668400	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr6:24665800-24668400	Active TSS	Fetal Brain Female	brain
22	chr6:24665800-24669800	Active TSS	A549	lung
23	chr6:24666000-24667800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:24666000-24667800	Active TSS	Brain Anterior Caudate	brain
25	chr6:24666000-24667800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr6:24666000-24667800	Active TSS	Right Ventricle	heart
27	chr6:24666000-24668000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:24666000-24668000	Active TSS	Aorta	Aorta
29	chr6:24666000-24668000	Active TSS	Ovary	ovary
30	chr6:24666000-24668200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr6:24666000-24668200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr6:24666000-24668200	Active TSS	Fetal Kidney	kidney
33	chr6:24666000-24668400	Active TSS	H1 Cell Line	embryonic stem cell
34	chr6:24666000-24668400	Active TSS	H9 Cell Line	embryonic stem cell
35	chr6:24666000-24668400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:24666000-24668400	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr6:24666000-24668400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:24666000-24668600	Active TSS	HSMM	muscle
39	chr6:24666000-24669600	Active TSS	K562	blood
40	chr6:24666200-24667800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:24666200-24667800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:24666200-24667800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr6:24666200-24667800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:24666200-24667800	Active TSS	Muscle Satellite Cultured Cells	--
45	chr6:24666200-24667800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:24666200-24667800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:24666200-24667800	Active TSS	Colon Smooth Muscle	Colon
48	chr6:24666200-24667800	Active TSS	Gastric	stomach
49	chr6:24666200-24667800	Active TSS	Placenta Amnion	Placenta Amnion
50	chr6:24666200-24667800	Active TSS	Small Intestine	intestine

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