Variant report

Variant	rs12267176
Chromosome Location	chr10:28031388-28031389
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:28031052-28031564	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr10:28031294-28031438	ProgFib	skin:	n/a	n/a
3	NRF1	chr10:28031106-28031433	GM12878	blood:	n/a	chr10:28031267-28031278 chr10:28031264-28031278 chr10:28031267-28031281 chr10:28031267-28031278
4	CTCF	chr10:28031300-28031450	HAc	cerebellar:	n/a	n/a
5	POLR2A	chr10:28031307-28031550	GM12878	blood:	n/a	n/a
6	PAX5	chr10:28031051-28031590	GM12878	blood:	n/a	chr10:28031228-28031237
7	NRF1	chr10:28031092-28031460	H1-hESC	embryonic stem cell:	n/a	chr10:28031267-28031278 chr10:28031264-28031278 chr10:28031267-28031281 chr10:28031267-28031278
8	RAD21	chr10:28031010-28031410	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr10:28031023-28031417	GM12878	blood:	n/a	n/a
10	MAX	chr10:28030999-28031634	ECC-1	luminal epithelium:	n/a	chr10:28031404-28031413
11	CEBPB	chr10:28031148-28031602	Hela-S3	cervix:	n/a	chr10:28031404-28031415
12	TCF3	chr10:28031097-28031598	GM12878	blood:	n/a	n/a
13	EP300	chr10:28030949-28031631	H1-hESC	embryonic stem cell:	n/a	chr10:28031401-28031415
14	RAD21	chr10:28031023-28031604	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr10:28030984-28031435	IMR90	lung:	n/a	n/a
16	TAF1	chr10:28030995-28031753	ECC-1	luminal epithelium:	n/a	n/a
17	RAD21	chr10:28030961-28031552	ECC-1	luminal epithelium:	n/a	n/a
18	RAD21	chr10:28030899-28031593	MCF-7	breast:	n/a	n/a
19	TBP	chr10:28031190-28031538	Hela-S3	cervix:	n/a	n/a
20	JUND	chr10:28031118-28031432	K562	blood:	n/a	chr10:28031366-28031378
21	TEAD4	chr10:28031072-28031543	ECC-1	luminal epithelium:	n/a	n/a
22	TEAD4	chr10:28031059-28031433	H1-hESC	embryonic stem cell:	n/a	n/a
23	CEBPB	chr10:28031175-28031595	IMR90	lung:	n/a	chr10:28031404-28031415
24	TCF7L2	chr10:28030795-28031455	Hela-S3	cervix:	n/a	chr10:28030972-28030981 chr10:28031142-28031149 chr10:28030972-28030982 chr10:28030968-28030984 chr10:28030971-28030980 chr10:28030969-28030983 chr10:28030968-28030984
25	ZNF143	chr10:28030910-28031457	H1-hESC	embryonic stem cell:	n/a	n/a
26	NFIC	chr10:28031095-28031577	GM12878	blood:	n/a	n/a
27	CEBPB	chr10:28031181-28031515	MCF-7	breast:	n/a	chr10:28031404-28031415
28	MAFK	chr10:28031097-28031512	Hela-S3	cervix:	n/a	n/a
29	HDAC2	chr10:28030983-28031459	MCF-7	breast:	n/a	n/a
30	POLR2A	chr10:28031254-28031509	SK-N-MC	brain:	n/a	n/a
31	CTCF	chr10:28030967-28031468	SK-N-SH	brain:	n/a	n/a
32	MTA3	chr10:28031158-28031547	GM12878	blood:	n/a	n/a
33	TCF7L2	chr10:28030746-28031528	HCT-116	colon:	n/a	chr10:28030972-28030981 chr10:28031142-28031149 chr10:28030972-28030982 chr10:28030968-28030984 chr10:28030971-28030980 chr10:28030969-28030983 chr10:28030968-28030984
34	RUNX3	chr10:28031126-28031577	GM12878	blood:	n/a	n/a
35	TEAD4	chr10:28030983-28031647	ECC-1	luminal epithelium:	n/a	n/a
36	TAF1	chr10:28031246-28031570	H1-hESC	embryonic stem cell:	n/a	n/a
37	TCF12	chr10:28031203-28031535	GM12878	blood:	n/a	chr10:28031522-28031529 chr10:28031518-28031528 chr10:28031521-28031531
38	NFATC1	chr10:28031169-28031486	GM12878	blood:	n/a	n/a
39	RAD21	chr10:28031004-28031459	IMR90	lung:	n/a	n/a
40	CEBPB	chr10:28031265-28031524	HepG2	liver:	n/a	chr10:28031404-28031415
41	GTF2F1	chr10:28031155-28031407	H1-hESC	embryonic stem cell:	n/a	n/a
42	RAD21	chr10:28030961-28031399	HepG2	liver:	n/a	n/a
43	ZNF143	chr10:28031060-28031503	GM12878	blood:	n/a	n/a
44	EBF1	chr10:28031265-28031465	GM12878	blood:	n/a	n/a
45	MAX	chr10:28030913-28031590	A549	lung:	n/a	chr10:28031404-28031413
46	EP300	chr10:28031222-28031524	GM12878	blood:	n/a	chr10:28031401-28031415
47	TCF7L2	chr10:28030735-28031656	PANC-1	pancreas:	n/a	chr10:28030972-28030981 chr10:28031142-28031149 chr10:28030972-28030982 chr10:28030968-28030984 chr10:28030971-28030980 chr10:28030969-28030983 chr10:28030968-28030984
48	HMGN3	chr10:28031059-28031778	K562	blood:	n/a	n/a
49	MYC	chr10:28031082-28031445	K562	blood:	n/a	chr10:28031404-28031413
50	BCLAF1	chr10:28031099-28031600	GM12878	blood:	n/a	chr10:28031585-28031598

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:28031385-28031435	PANC-1	pancreas:	n/a
2	chr10:28031385-28031435	HEK293	kidney:	embryo
3	chr10:28031385-28031435	AG10803	skin:	n/a
4	chr10:28031385-28031435	SK-N-MC	brain:	n/a
5	chr10:28031385-28031435	NT2-D1	testis:	n/a
6	chr10:28031385-28031435	HCT-116	colon:	n/a
7	chr10:28031385-28031435	U87	brain:	n/a
8	chr10:28031385-28031435	AoSMC	blood vessel:	n/a
9	chr10:28031385-28031435	Hela-S3	cervix:	n/a
10	chr10:28031385-28031435	Hepatocyte	liver:	n/a
11	chr10:28031385-28031435	BE2_C	brain:	n/a
12	chr10:28031385-28031435	SK-N-SH	brain:	n/a
13	chr10:28031385-28031435	PrEC	prostate:	n/a
14	chr10:28031385-28031435	AG09319	gingival:	n/a
15	chr10:28031385-28031435	HAEpiC	amniotic membrane:	n/a
16	chr10:28031385-28031435	GM19239	blood:	n/a
17	chr10:28031385-28031435	ovcar-3	ovarian:	n/a
18	chr10:28031385-28031435	AG04450	lung:	fetal
19	chr10:28031385-28031435	Caco-2	colon:	n/a
20	chr10:28031385-28031435	HRE	kidney:	n/a
21	chr10:28031385-28031435	AG04449	skin:	fetal
22	chr10:28031385-28031435	BJ	skin:	n/a
23	chr10:28031385-28031435	IMR90	lung:	fetal
24	chr10:28031385-28031435	MCF10A-Er-Src	breast:	n/a
25	chr10:28031385-28031435	HRCEpiC	kidney:	n/a
26	chr10:28031385-28031435	GM12892	blood:	n/a
27	chr10:28031385-28031435	MCF-7	breast:	n/a
28	chr10:28031385-28031435	ECC-1	luminal epithelium:	n/a
29	chr10:28031385-28031435	HNPCEpiC	eye:	n/a
30	chr10:28031385-28031435	SKMC	muscle:	n/a
31	chr10:28031385-28031435	HCF	heart:	n/a
32	chr10:28031385-28031435	HCM	heart:	n/a
33	chr10:28031385-28031435	A549	lung:	n/a
34	chr10:28031385-28031435	HEEpiC	esophagus:	n/a
35	chr10:28031385-28031435	T-47D	breast:	n/a
36	chr10:28031385-28031435	HIPEpiC	eye:	n/a
37	chr10:28031385-28031435	NHDF-neo	bronchial:	n/a
38	chr10:28031385-28031435	Jurkat	blood:	n/a
39	chr10:28031385-28031435	HCPEpiC	choroid plexus:	n/a
40	chr10:28031385-28031435	NH-A	brain:	n/a
41	chr10:28031385-28031435	HMEC	breast:	n/a
42	chr10:28031385-28031435	K562	blood:	n/a
43	chr10:28031385-28031435	LNCaP	prostate:	n/a
44	chr10:28031385-28031435	NHBE	bronchial:	n/a
45	chr10:28031385-28031435	HL-60	blood:	n/a
46	chr10:28031385-28031435	ProgFib	skin:	n/a
47	chr10:28031385-28031435	SAEC	small airway:	n/a
48	chr10:28031385-28031435	RPTEC	kidney:	n/a
49	chr10:28031385-28031435	HepG2	liver:	n/a
50	chr10:28031385-28031435	GM06990	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:28030500..28032197-chr10:28034707..28036331,2	MCF-7	breast:
2	chr10:28030939..28031493-chr10:28468370..28469079,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230500	TF binding region
ENSG00000230500	CpG island
ENSG00000150051	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12241763	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12243231	0.85[AMR][1000 genomes]
rs12249445	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12257693	0.80[AFR][1000 genomes]
rs12263640	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12265151	0.85[AMR][1000 genomes]
rs60120536	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368825	chr10:27864181-28043820	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv831813	chr10:28017606-28200651	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28029800-28032600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr10:28029800-28033200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr10:28029800-28035800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr10:28029800-28036000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr10:28030000-28032800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:28030000-28033400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:28030000-28033600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr10:28030000-28036600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr10:28030200-28031400	Bivalent Enhancer	Fetal Heart	heart
10	chr10:28030200-28031800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:28030200-28032800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:28030200-28036200	Bivalent Enhancer	Fetal Brain Male	brain
13	chr10:28030200-28036400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr10:28030400-28031600	Bivalent/Poised TSS	Thymus	Thymus
15	chr10:28030400-28031800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:28030400-28032200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:28030400-28033200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
18	chr10:28030400-28033400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr10:28030600-28032200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
20	chr10:28030600-28032800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:28030600-28033200	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr10:28030600-28035400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:28030800-28031400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
24	chr10:28030800-28031400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr10:28030800-28031600	Bivalent/Poised TSS	Fetal Kidney	kidney
26	chr10:28030800-28031800	Bivalent/Poised TSS	HepG2	liver
27	chr10:28030800-28032000	Bivalent/Poised TSS	A549	lung
28	chr10:28030800-28032600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
29	chr10:28030800-28032800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:28030800-28032800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
31	chr10:28030800-28033000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
32	chr10:28030800-28033400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
33	chr10:28030800-28033800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr10:28030800-28035000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
35	chr10:28030800-28035600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
36	chr10:28030800-28035800	Active TSS	Aorta	Aorta
37	chr10:28031000-28031400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:28031000-28031400	Active TSS	Colon Smooth Muscle	Colon
39	chr10:28031000-28031600	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr10:28031000-28031600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:28031000-28031600	Active TSS	Right Ventricle	heart
42	chr10:28031000-28031800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr10:28031000-28031800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr10:28031000-28031800	Active TSS	Lung	lung
45	chr10:28031000-28031800	Active TSS	Pancreas	Pancrea
46	chr10:28031000-28031800	Active TSS	HSMM	muscle
47	chr10:28031000-28032000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
48	chr10:28031000-28032200	Active TSS	Rectal Smooth Muscle	rectum
49	chr10:28031000-28032200	Active TSS	Hela-S3	cervix
50	chr10:28031000-28032400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood

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