Variant report

Variant	rs12197755
Chromosome Location	chr6:45387495-45387496
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:168)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:168 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:45387115-45387829	MCF-7	breast:	n/a	n/a
2	CTCF	chr6:45387222-45387614	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr6:45387153-45387669	A549	lung:	n/a	chr6:45387625-45387637
4	CTCF	chr6:45387171-45387506	HepG2	liver:	n/a	n/a
5	CTCF	chr6:45387179-45387707	K562	blood:	n/a	n/a
6	CTCF	chr6:45387360-45387510	GM06990	blood:	n/a	n/a
7	BHLHE40	chr6:45387189-45387619	K562	blood:	n/a	n/a
8	CTCF	chr6:45387327-45387502	GM19239	blood:	n/a	n/a
9	RAD21	chr6:45387213-45387517	GM12878	blood:	n/a	n/a
10	TBP	chr6:45387304-45387770	H1-hESC	embryonic stem cell:	n/a	n/a
11	GATA3	chr6:45387133-45387791	MCF-7	breast:	n/a	chr6:45387178-45387188
12	CTCF	chr6:45387296-45387556	Gliobla	brain:	n/a	n/a
13	CTCF	chr6:45387360-45387510	HMF	breast:	n/a	n/a
14	ZEB1	chr6:45387391-45387652	GM12878	blood:	n/a	n/a
15	RAD21	chr6:45387152-45387639	HepG2	liver:	n/a	chr6:45387625-45387637
16	RAD21	chr6:45387192-45387931	H1-hESC	embryonic stem cell:	n/a	chr6:45387625-45387637
17	CTCF	chr6:45387264-45387586	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr6:45387274-45387655	MCF-7	breast:	n/a	n/a
19	CTCF	chr6:45387440-45387590	GM12869	blood:	n/a	n/a
20	MYC	chr6:45387246-45387578	K562	blood:	n/a	n/a
21	CTCF	chr6:45387360-45387510	HRE	kidney:	n/a	n/a
22	CTCF	chr6:45387360-45387510	HPF	lung:	n/a	n/a
23	CTCF	chr6:45387257-45387628	NHEK	skin:	n/a	n/a
24	CTCF	chr6:45387274-45387670	GM12891	blood:	n/a	n/a
25	CTCF	chr6:45387360-45387510	HCM	heart:	n/a	n/a
26	CTCF	chr6:45387251-45387702	MCF-7	breast:	n/a	n/a
27	BHLHE40	chr6:45387328-45387528	GM12878	blood:	n/a	n/a
28	MAZ	chr6:45387252-45387612	K562	blood:	n/a	n/a
29	CTCF	chr6:45387264-45387683	MCF-7	breast:	n/a	n/a
30	CTCF	chr6:45387400-45387550	GM12875	blood:	n/a	n/a
31	RAD21	chr6:45387122-45387671	A549	lung:	n/a	chr6:45387625-45387637
32	RCOR1	chr6:45387081-45387607	K562	blood:	n/a	n/a
33	MAX	chr6:45387234-45387744	ECC-1	luminal epithelium:	n/a	n/a
34	UBTF	chr6:45387311-45387549	K562	blood:	n/a	n/a
35	CCNT2	chr6:45387328-45387566	K562	blood:	n/a	n/a
36	ZNF143	chr6:45387274-45387505	H1-hESC	embryonic stem cell:	n/a	n/a
37	MYC	chr6:45387223-45387587	K562	blood:	n/a	n/a
38	E2F6	chr6:45387347-45387878	H1-hESC	embryonic stem cell:	n/a	chr6:45387652-45387664
39	NR2F2	chr6:45387177-45387815	MCF-7	breast:	n/a	n/a
40	CTCF	chr6:45387206-45387627	GM12878	blood:	n/a	n/a
41	HDAC2	chr6:45387141-45387864	MCF-7	breast:	n/a	chr6:45387166-45387180 chr6:45387160-45387174 chr6:45387162-45387176 chr6:45387159-45387173
42	CTCF	chr6:45387355-45387513	Kidney_OC	kidney:	n/a	n/a
43	CTCF	chr6:45387300-45387536	GM12892	blood:	n/a	n/a
44	CTCF	chr6:45387293-45387552	LNCaP	prostate:	n/a	n/a
45	CTCF	chr6:45387360-45387510	HMEC	breast:	n/a	n/a
46	ZNF217	chr6:45387402-45387642	MCF-7	breast:	n/a	n/a
47	GATA3	chr6:45387241-45387689	T-47D	breast:	n/a	n/a
48	TCF12	chr6:45387389-45387594	H1-hESC	embryonic stem cell:	n/a	chr6:45387580-45387587
49	CTCF	chr6:45387018-45387806	SK-N-SH	brain:	n/a	n/a
50	CTCF	chr6:45387360-45387510	GM12864	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:45054176..45055264-chr6:45386958..45387535,3	MCF-7	breast:
2	chr6:45343194..45347445-chr6:45386856..45389425,4	MCF-7	breast:
3	chr6:45385643..45388546-chr6:45402027..45403903,2	K562	blood:
4	chr6:45385112..45387684-chr6:45388675..45391709,3	MCF-7	breast:
5	chr6:44621438..44623552-chr6:45385736..45388859,3	MCF-7	breast:
6	chr6:44623198..44623814-chr6:45386958..45387878,2	MCF-7	breast:
7	chr6:44622930..44623850-chr6:45387025..45387858,4	K562	blood:
8	chr6:45054220..45054815-chr6:45386791..45387562,3	MCF-7	breast:
9	chr6:44623011..44624037-chr6:45386769..45387720,3	MCF-7	breast:
10	chr6:45343131..45346998-chr6:45386286..45389886,4	MCF-7	breast:

No data

Variant related genes	Relation type
RUNX2	TF binding region
ENSG00000124813	Chromatin interaction
ENSG00000271857	Chromatin interaction
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10456549	0.82[CEU][hapmap]
rs10456553	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948220	0.83[CEU][hapmap]
rs10948226	0.83[CEU][hapmap]
rs10948233	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11964690	0.82[CEU][hapmap]
rs11966878	0.82[CEU][hapmap]
rs12191262	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs12191751	0.83[CEU][hapmap]
rs12192267	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194628	0.83[CEU][hapmap]
rs12199871	1.00[YRI][hapmap]
rs12201563	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12201899	0.82[CEU][hapmap]
rs12203052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203466	0.83[CEU][hapmap]
rs12205523	0.82[CEU][hapmap]
rs12210230	0.83[CEU][hapmap]
rs12211510	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12216308	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs1321078	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1321079	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1321080	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17209741	0.82[CEU][hapmap]
rs17209769	0.82[CEU][hapmap]
rs17209895	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17288250	0.83[CEU][hapmap]
rs17288257	0.83[CEU][hapmap]
rs17288320	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17288327	0.82[CEU][hapmap]
rs1852983	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1852984	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2064628	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894641	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4267941	0.83[CEU][hapmap]
rs4400216	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4443508	0.83[CEU][hapmap]
rs4479922	0.83[CEU][hapmap]
rs62400353	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927213	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs72862930	0.89[AMR][1000 genomes];0.87[EUR][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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45384800-45388000	Weak transcription	Hela-S3	cervix
2	chr6:45386800-45389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:45386800-45389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:45387000-45387800	Bivalent/Poised TSS	Primary T helper naive cells from peripheral blood	blood
5	chr6:45387000-45388400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:45387000-45388800	Flanking Active TSS	NH-A	brain
7	chr6:45387000-45389000	Flanking Active TSS	Osteobl	bone
8	chr6:45387000-45389400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr6:45387000-45389800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr6:45387000-45391800	Bivalent Enhancer	Fetal Brain Male	brain
11	chr6:45387000-45392200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:45387200-45387600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:45387200-45387600	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:45387200-45387600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
15	chr6:45387200-45387600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:45387200-45387600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:45387200-45387600	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr6:45387200-45387600	Flanking Bivalent TSS/Enh	Placenta	Placenta
19	chr6:45387200-45387600	Bivalent/Poised TSS	A549	lung
20	chr6:45387200-45387600	Bivalent Enhancer	HUVEC	blood vessel
21	chr6:45387200-45387600	Active TSS	K562	blood
22	chr6:45387200-45387800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:45387200-45387800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:45387200-45387800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr6:45387200-45387800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
26	chr6:45387200-45387800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
27	chr6:45387200-45387800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
28	chr6:45387200-45387800	Bivalent/Poised TSS	Fetal Kidney	kidney
29	chr6:45387200-45387800	Bivalent Enhancer	Psoas Muscle	Psoas
30	chr6:45387200-45387800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr6:45387200-45387800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
32	chr6:45387200-45387800	Active TSS	NHDF-Ad	bronchial
33	chr6:45387200-45388000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr6:45387200-45388000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:45387200-45388000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:45387200-45388000	Active TSS	Brain Substantia Nigra	brain
37	chr6:45387200-45388000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
38	chr6:45387200-45388200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:45387200-45388200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:45387200-45388200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
43	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	Liver	Liver
44	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
45	chr6:45387200-45388200	Flanking Active TSS	Ovary	ovary
46	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	Sigmoid Colon	Sigmoid Colon
47	chr6:45387200-45388200	Enhancers	Spleen	Spleen
48	chr6:45387200-45388400	Bivalent Enhancer	Stomach Mucosa	stomach
49	chr6:45387200-45388600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:45387200-45388600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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