Variant report

Variant	rs12554060
Chromosome Location	chr9:94712624-94712625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:262)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:262 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr9:94712498-94712698	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr9:94712399-94712775	GM12878	blood:	n/a	n/a
3	RAD21	chr9:94712248-94713089	SK-N-SH_RA	brain:	n/a	chr9:94713037-94713050
4	CTCF	chr9:94712017-94712822	H1-hESC	embryonic stem cell:	n/a	n/a
5	RCOR1	chr9:94712419-94712991	K562	blood:	n/a	n/a
6	CTCF	chr9:94712520-94712670	HL-60	blood:	n/a	n/a
7	CTCF	chr9:94712454-94712722	GM12891	blood:	n/a	n/a
8	CTCF	chr9:94712540-94712690	GM12873	blood:	n/a	n/a
9	CTCF	chr9:94712496-94712677	GM20000	blood:	n/a	n/a
10	POLR2A	chr9:94712005-94712882	K562	blood:	n/a	n/a
11	SIN3A	chr9:94712003-94713013	H1-hESC	embryonic stem cell:	n/a	chr9:94712053-94712066
12	MAZ	chr9:94710719-94713473	IMR90	lung:	n/a	chr9:94710846-94710856
13	HCFC1	chr9:94712161-94712974	K562	blood:	n/a	n/a
14	CTCF	chr9:94712520-94712670	RPTEC	kidney:	n/a	n/a
15	CTCF	chr9:94712520-94712670	GM12864	blood:	n/a	n/a
16	POLR2A	chr9:94712375-94712786	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr9:94712473-94712746	Fibrobl	skin:	n/a	n/a
18	CREB1	chr9:94712395-94712789	A549	lung:	n/a	n/a
19	E2F6	chr9:94712374-94712719	K562	blood:	n/a	n/a
20	CTCF	chr9:94712520-94712670	HVMF	connective:	n/a	n/a
21	FOXP2	chr9:94712430-94712674	PFSK-1	brain:	n/a	n/a
22	CTCF	chr9:94712483-94712690	LNCaP	prostate:	n/a	n/a
23	ZMIZ1	chr9:94712412-94712844	K562	blood:	n/a	n/a
24	CTCF	chr9:94712500-94712650	AG04450	lung:	n/a	n/a
25	CTCF	chr9:94712422-94712681	HepG2	liver:	n/a	n/a
26	POLR2A	chr9:94711919-94712859	K562	blood:	n/a	n/a
27	CTCF	chr9:94712500-94712650	GM12869	blood:	n/a	n/a
28	CTCF	chr9:94712540-94712690	HRPEpiC	eye:	n/a	n/a
29	BACH1	chr9:94712501-94712871	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr9:94712500-94712650	GM12873	blood:	n/a	n/a
31	CTCF	chr9:94712500-94712650	HAc	cerebellar:	n/a	n/a
32	MXI1	chr9:94710177-94713341	SK-N-SH	brain:	n/a	n/a
33	TCF7L2	chr9:94712302-94713026	HCT-116	colon:	n/a	n/a
34	CTCF	chr9:94712495-94712724	GM12878	blood:	n/a	n/a
35	GABPA	chr9:94712333-94712684	K562	blood:	n/a	n/a
36	CTCF	chr9:94712480-94712630	HPAF	blood vessel:	n/a	n/a
37	ZBTB7A	chr9:94711005-94712853	K562	blood:	n/a	n/a
38	MYC	chr9:94712494-94712659	K562	blood:	n/a	n/a
39	MYC	chr9:94711906-94712738	K562	blood:	n/a	n/a
40	UBTF	chr9:94710450-94712833	K562	blood:	n/a	n/a
41	POLR2A	chr9:94710760-94712921	K562	blood:	n/a	n/a
42	RAD21	chr9:94712512-94712712	HepG2	liver:	n/a	n/a
43	CTCF	chr9:94712427-94712732	K562	blood:	n/a	n/a
44	CTCF	chr9:94712496-94712654	HUVEC	blood vessel:	n/a	n/a
45	RAD21	chr9:94712253-94712824	IMR90	lung:	n/a	n/a
46	SMC3	chr9:94712049-94713651	SK-N-SH	brain:	n/a	chr9:94712523-94712533 chr9:94712653-94712663
47	CTCF	chr9:94712520-94712670	GM12865	blood:	n/a	n/a
48	CTCF	chr9:94712500-94712650	AG09319	gingival:	n/a	n/a
49	CTCF	chr9:94712520-94712670	GM12867	blood:	n/a	n/a
50	YY1	chr9:94712349-94712758	HepG2	liver:	n/a	chr9:94712542-94712553 chr9:94712419-94712433 chr9:94712475-94712486

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:94537481..94538450-chr9:94712230..94712819,2	MCF-7	breast:
2	chr9:94496411..94497072-chr9:94712544..94713048,2	MCF-7	breast:
3	chr9:94537447..94538880-chr9:94712081..94713098,9	MCF-7	breast:
4	chr9:94537694..94538378-chr9:94712239..94713033,2	K562	blood:

No data

Variant related genes	Relation type
ROR2	TF binding region
ENSG00000169071	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10820926	0.87[AMR][1000 genomes]
rs10820927	0.87[AMR][1000 genomes]
rs10820929	0.87[AMR][1000 genomes]
rs10992176	0.83[AMR][1000 genomes]
rs10992177	0.87[AMR][1000 genomes]
rs10992178	0.81[AMR][1000 genomes]
rs10992179	0.87[AMR][1000 genomes]
rs10992180	0.83[AMR][1000 genomes]
rs10992183	0.87[AMR][1000 genomes]
rs12236121	0.87[AMR][1000 genomes]
rs12238682	0.82[AMR][1000 genomes]
rs16908021	0.82[AMR][1000 genomes]
rs1892267	0.80[AMR][1000 genomes]
rs4504700	0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv982625	chr9:94702344-94712887	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3359987	chr9:94710956-94713704	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr9:94709200-94713200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:94709800-94713200	Active TSS	Fetal Kidney	kidney
3	chr9:94710000-94712800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:94710000-94712800	Active TSS	K562	blood
5	chr9:94710000-94714000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:94710200-94713000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr9:94710200-94713200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:94710200-94713200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr9:94710200-94713200	Active TSS	Colon Smooth Muscle	Colon
10	chr9:94710400-94713000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:94710400-94713200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:94710400-94713200	Active TSS	Fetal Lung	lung
13	chr9:94710400-94713400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr9:94710600-94712800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:94710600-94712800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr9:94710600-94712800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:94710600-94713000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr9:94710600-94713200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr9:94710600-94713200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
20	chr9:94710600-94713200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr9:94710600-94713400	Active TSS	Ovary	ovary
22	chr9:94710800-94712800	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr9:94710800-94712800	Bivalent/Poised TSS	Thymus	Thymus
24	chr9:94710800-94713000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:94710800-94713000	Active TSS	Rectal Smooth Muscle	rectum
26	chr9:94710800-94713200	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:94710800-94713200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:94710800-94713200	Bivalent/Poised TSS	A549	lung
29	chr9:94710800-94713400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
30	chr9:94710800-94713400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
31	chr9:94711000-94712800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:94711000-94712800	Enhancers	Primary B cells from cord blood	blood
33	chr9:94711000-94712800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:94711000-94712800	Bivalent/Poised TSS	Fetal Stomach	stomach
35	chr9:94711000-94713000	Active TSS	Gastric	stomach
36	chr9:94711000-94713000	Bivalent/Poised TSS	Psoas Muscle	Psoas
37	chr9:94711000-94713000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
38	chr9:94711000-94713000	Active TSS	Hela-S3	cervix
39	chr9:94711000-94713200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr9:94711000-94713200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:94711000-94713200	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr9:94711000-94713200	Bivalent/Poised TSS	HSMM	muscle
43	chr9:94711000-94713400	Active TSS	Stomach Smooth Muscle	stomach
44	chr9:94711000-94713400	Bivalent/Poised TSS	NHDF-Ad	bronchial
45	chr9:94711200-94712800	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr9:94711200-94713200	Bivalent Enhancer	Fetal Brain Male	brain
47	chr9:94711200-94713200	Active TSS	Placenta Amnion	Placenta Amnion
48	chr9:94711200-94713200	Active TSS	NHLF	lung
49	chr9:94711200-94713200	Bivalent/Poised TSS	Osteobl	bone
50	chr9:94711200-94717000	Weak transcription	Fetal Heart	heart

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