Variant report

Variant	rs28435255
Chromosome Location	chr12:122020881-122020882
allele	A/G
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	CHD1	chr12:122019587-122020967	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr12:122020639-122021392	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr12:122020006-122021044	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF7L2	chr12:122020569-122020973	Hela-S3	cervix:	n/a	chr12:122020752-122020761
5	POLR2A	chr12:122019572-122021238	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr12:122020422-122020989	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIN3AK20	chr12:122018029-122020954	H1-hESC	embryonic stem cell:	n/a	n/a
8	TEAD4	chr12:122020466-122021084	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF12	chr12:122020529-122021015	H1-hESC	embryonic stem cell:	n/a	n/a
10	EP300	chr12:122020614-122020925	K562	blood:	n/a	chr12:122020724-122020738
11	EP300	chr12:122020419-122021050	H1-hESC	embryonic stem cell:	n/a	chr12:122020724-122020738
12	EP300	chr12:122020541-122020924	H1-hESC	embryonic stem cell:	n/a	chr12:122020724-122020738
13	MYC	chr12:122020170-122021192	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUN	chr12:122020633-122020946	K562	blood:	n/a	n/a
15	YY1	chr12:122019866-122021094	H1-hESC	embryonic stem cell:	n/a	n/a
16	HDAC2	chr12:122020547-122020932	H1-hESC	embryonic stem cell:	n/a	n/a
17	EP300	chr12:122020708-122020905	HepG2	liver:	n/a	chr12:122020724-122020738
18	JUND	chr12:122020527-122020911	K562	blood:	n/a	chr12:122020698-122020709
19	BCL11A	chr12:122020635-122020901	H1-hESC	embryonic stem cell:	n/a	chr12:122020651-122020664
20	TEAD4	chr12:122020468-122021140	H1-hESC	embryonic stem cell:	n/a	n/a
21	SP4	chr12:122020413-122021026	H1-hESC	embryonic stem cell:	n/a	n/a
22	TEAD4	chr12:122020540-122020974	K562	blood:	n/a	n/a
23	TCF7L2	chr12:122020434-122021139	HepG2	liver:	n/a	chr12:122021067-122021083 chr12:122020752-122020761
24	FOS	chr12:122020462-122020997	HUVEC	blood vessel:	n/a	chr12:122020698-122020709
25	JUND	chr12:122020534-122020892	H1-hESC	embryonic stem cell:	n/a	chr12:122020698-122020709
26	JUND	chr12:122020299-122021187	H1-hESC	embryonic stem cell:	n/a	chr12:122020698-122020709
27	CEBPB	chr12:122020616-122021280	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF7	chr12:122019836-122021304	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr12:122019556-122021300	H1-hESC	embryonic stem cell:	n/a	chr12:122019709-122019717
30	CTBP2	chr12:122020413-122020947	H1-hESC	embryonic stem cell:	n/a	n/a
31	EGR1	chr12:122020560-122020902	K562	blood:	n/a	n/a
32	POLR2A	chr12:122020620-122020886	HUVEC	blood vessel:	n/a	n/a
33	EGR1	chr12:122020589-122020989	H1-hESC	embryonic stem cell:	n/a	n/a
34	TCF7L2	chr12:122020722-122020895	PANC-1	pancreas:	n/a	chr12:122020752-122020761
35	CHD2	chr12:122020841-122020968	K562	blood:	n/a	n/a
36	TBL1XR1	chr12:122020580-122020909	K562	blood:	n/a	n/a
37	EP300	chr12:122020462-122020925	HepG2	liver:	n/a	chr12:122020724-122020738
38	SIN3AK20	chr12:122020607-122020958	H1-hESC	embryonic stem cell:	n/a	n/a
39	ZNF143	chr12:122020493-122020972	H1-hESC	embryonic stem cell:	n/a	n/a
40	SP1	chr12:122020342-122021157	H1-hESC	embryonic stem cell:	n/a	n/a
41	RCOR1	chr12:122020566-122020920	K562	blood:	n/a	n/a
42	CUX1	chr12:122020518-122020918	K562	blood:	n/a	n/a
43	POLR2A	chr12:122020434-122021205	H1-hESC	embryonic stem cell:	n/a	n/a
44	SP1	chr12:122020399-122021095	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr12:122017817-122021420	H1-hESC	embryonic stem cell:	n/a	n/a
46	SIN3A	chr12:122017791-122021030	H1-hESC	embryonic stem cell:	n/a	chr12:122018963-122018974
47	TAF1	chr12:122020392-122021148	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr12:122015308-122021316	H1-hESC	embryonic stem cell:	n/a	n/a
49	ATF2	chr12:122020349-122021357	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr12:122019817-122021370	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122014421..122021664-chr12:122061311..122067896,12	MCF-7	breast:
2	chr12:122018588..122021080-chr12:122238013..122240517,2	MCF-7	breast:
3	chr12:122016252..122018174-chr12:122019447..122021740,2	MCF-7	breast:
4	chr12:122019678..122022044-chr12:122055209..122057856,2	K562	blood:

Variant related genes	Relation type
KDM2B	TF binding region
ENSG00000089094	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000182500	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10840610	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10840651	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11043181	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12304179	0.85[EUR][1000 genomes]
rs12315280	0.85[EUR][1000 genomes]
rs12319633	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28397246	0.83[AMR][1000 genomes]
rs28489288	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28517331	0.84[AMR][1000 genomes]
rs28552516	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28594507	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73227906	0.82[AMR][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	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122014200-122021200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:122014800-122021000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:122014800-122021000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:122015400-122021000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:122015600-122021800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:122015800-122021000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:122016000-122021000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:122017200-122021200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:122018600-122021000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:122018600-122021000	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr12:122018600-122021000	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr12:122018600-122021400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:122019000-122021200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:122019200-122021000	Enhancers	Fetal Intestine Large	intestine
15	chr12:122019400-122021000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:122019400-122021000	Enhancers	Fetal Stomach	stomach
17	chr12:122019400-122021200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:122019600-122021000	Weak transcription	Pancreas	Pancrea
19	chr12:122019800-122021200	Enhancers	Fetal Thymus	thymus
20	chr12:122019800-122021800	Enhancers	A549	lung
21	chr12:122019800-122023000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:122020000-122021000	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr12:122020000-122021000	Weak transcription	Spleen	Spleen
24	chr12:122020000-122021200	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:122020000-122021200	Enhancers	Fetal Muscle Leg	muscle
26	chr12:122020000-122021400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr12:122020000-122022000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr12:122020200-122021000	Active TSS	H1 Cell Line	embryonic stem cell
29	chr12:122020200-122021000	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr12:122020200-122021000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:122020200-122021000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr12:122020200-122021000	Enhancers	Adipose Nuclei	Adipose
33	chr12:122020200-122021000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr12:122020200-122021000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr12:122020200-122021000	Enhancers	Fetal Intestine Small	intestine
36	chr12:122020200-122021000	Enhancers	Stomach Mucosa	stomach
37	chr12:122020200-122021000	Enhancers	Thymus	Thymus
38	chr12:122020200-122021000	Enhancers	HSMMtube	muscle
39	chr12:122020200-122021000	Enhancers	NHDF-Ad	bronchial
40	chr12:122020200-122021200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:122020200-122021200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr12:122020200-122021200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:122020200-122021200	Enhancers	Aorta	Aorta
44	chr12:122020200-122021200	Enhancers	Fetal Lung	lung
45	chr12:122020200-122021200	Enhancers	Osteobl	bone
46	chr12:122020200-122021800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:122020200-122022200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:122020200-122022200	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr12:122020200-122022400	Enhancers	Fetal Heart	heart
50	chr12:122020200-122027800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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