Variant report

Variant	rs28397246
Chromosome Location	chr12:122019849-122019850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

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	KAP1	chr12:122018828-122020250	U2OS	brain:	n/a	n/a
3	POLR2A	chr12:122019572-122021238	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3AK20	chr12:122018029-122020954	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr12:122017050-122020876	SK-N-SH	brain:	n/a	n/a
6	MYC	chr12:122019777-122019852	HepG2	liver:	n/a	n/a
7	WRNIP1	chr12:122019140-122019986	GM12878	blood:	n/a	n/a
8	BHLHE40	chr12:122018861-122020340	K562	blood:	n/a	n/a
9	GATA1	chr12:122018806-122020867	PBDE	blood:	n/a	chr12:122020736-122020753 chr12:122019496-122019505 chr12:122020731-122020747
10	MTA3	chr12:122018311-122020270	GM12878	blood:	n/a	n/a
11	TAF7	chr12:122019836-122021304	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAZ	chr12:122017960-122019867	K562	blood:	n/a	chr12:122019709-122019717 chr12:122018156-122018166
13	MAX	chr12:122019556-122021300	H1-hESC	embryonic stem cell:	n/a	chr12:122019709-122019717
14	EGR1	chr12:122019819-122020010	K562	blood:	n/a	n/a
15	RCOR1	chr12:122018844-122019919	K562	blood:	n/a	n/a
16	ATF2	chr12:122019408-122020282	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZNF263	chr12:122019259-122020136	HEK293-T-REx	kidney:	n/a	n/a
18	MYC	chr12:122017902-122019964	K562	blood:	n/a	chr12:122019709-122019717 chr12:122018156-122018166
19	MYC	chr12:122019135-122020304	K562	blood:	n/a	chr12:122019709-122019717
20	POLR2A	chr12:122017817-122021420	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3A	chr12:122017791-122021030	H1-hESC	embryonic stem cell:	n/a	chr12:122018963-122018974
22	POLR2A	chr12:122018711-122020303	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr12:122015308-122021316	H1-hESC	embryonic stem cell:	n/a	n/a
24	CUX1	chr12:122019391-122020048	K562	blood:	n/a	n/a
25	MAX	chr12:122019817-122021370	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr12:122019722-122020464	SK-N-SH	brain:	n/a	n/a
27	TEAD4	chr12:122018736-122019912	K562	blood:	n/a	n/a
28	NR2F2	chr12:122018730-122020208	K562	blood:	n/a	n/a
29	EP300	chr12:122019130-122019849	K562	blood:	n/a	n/a
30	MXI1	chr12:122019357-122020339	GM12878	blood:	n/a	n/a
31	MAX	chr12:122019827-122020339	K562	blood:	n/a	n/a
32	CBX3	chr12:122018989-122019905	K562	blood:	n/a	n/a
33	MAX	chr12:122019760-122020445	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr12:122019424-122021014	PFSK-1	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122017334..122020292-chr12:122231782..122234542,4	K562	blood:
2	chr12:122014421..122021664-chr12:122061311..122067896,12	MCF-7	breast:
3	chr12:122018588..122021080-chr12:122238013..122240517,2	MCF-7	breast:
4	chr12:122018621..122020135-chr12:122041419..122043221,2	K562	blood:
5	chr12:121973453..121977492-chr12:122016919..122020388,4	K562	blood:
6	chr12:122016252..122018174-chr12:122019447..122021740,2	MCF-7	breast:
7	chr12:122019678..122022044-chr12:122055209..122057856,2	K562	blood:

No data

Variant related genes	Relation type
KDM2B	TF binding region
ENSG00000212694	Chromatin interaction
ENSG00000182500	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000252393	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28378998	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28435255	0.83[AMR][1000 genomes]
rs28508138	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28517331	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28546504	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73227906	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227912	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[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	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:119 , 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	chr12:122014600-122020600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr12:122014600-122020600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:122014800-122020800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:122014800-122021000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:122014800-122021000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:122015400-122021000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:122015600-122020200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr12:122015600-122021800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:122015800-122021000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:122016000-122021000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:122016200-122020200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:122016400-122020400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:122017200-122021200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:122018400-122020000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:122018400-122020200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr12:122018400-122020400	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr12:122018400-122020800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:122018600-122020000	Flanking Active TSS	Primary B cells from peripheral blood	blood
20	chr12:122018600-122020000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:122018600-122020000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:122018600-122020000	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr12:122018600-122020000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr12:122018600-122020000	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr12:122018600-122020200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr12:122018600-122020200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr12:122018600-122020200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr12:122018600-122020200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr12:122018600-122020200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:122018600-122020200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:122018600-122020200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:122018600-122020200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr12:122018600-122020200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr12:122018600-122020200	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr12:122018600-122020200	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr12:122018600-122020200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr12:122018600-122020200	Flanking Active TSS	Thymus	Thymus
38	chr12:122018600-122020200	Flanking Active TSS	Osteobl	bone
39	chr12:122018600-122020400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:122018600-122020400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr12:122018600-122020400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr12:122018600-122020600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr12:122018600-122020600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr12:122018600-122020600	Flanking Active TSS	HUVEC	blood vessel
45	chr12:122018600-122020600	Flanking Active TSS	NH-A	brain
46	chr12:122018600-122020800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr12:122018600-122020800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr12:122018600-122020800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr12:122018600-122020800	Flanking Active TSS	Dnd41	blood
50	chr12:122018600-122020800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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