Variant report

Variant	rs28517331
Chromosome Location	chr12:122020661-122020662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:93)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:93 , 50 per page) page: 1 2

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	USF2	chr12:122020055-122020878	H1-hESC	embryonic stem cell:	n/a	n/a
7	TAF1	chr12:122020422-122020989	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3AK20	chr12:122018029-122020954	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr12:122020466-122021084	H1-hESC	embryonic stem cell:	n/a	n/a
10	TCF12	chr12:122020529-122021015	H1-hESC	embryonic stem cell:	n/a	n/a
11	EP300	chr12:122020614-122020925	K562	blood:	n/a	chr12:122020724-122020738
12	EP300	chr12:122020419-122021050	H1-hESC	embryonic stem cell:	n/a	chr12:122020724-122020738
13	EP300	chr12:122020541-122020924	H1-hESC	embryonic stem cell:	n/a	chr12:122020724-122020738
14	MYC	chr12:122020170-122021192	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUN	chr12:122020633-122020946	K562	blood:	n/a	n/a
16	YY1	chr12:122019866-122021094	H1-hESC	embryonic stem cell:	n/a	n/a
17	HDAC2	chr12:122020547-122020932	H1-hESC	embryonic stem cell:	n/a	n/a
18	ARID3A	chr12:122020633-122020806	K562	blood:	n/a	n/a
19	MXI1	chr12:122017050-122020876	SK-N-SH	brain:	n/a	n/a
20	JUND	chr12:122020527-122020911	K562	blood:	n/a	chr12:122020698-122020709
21	BCL11A	chr12:122020635-122020901	H1-hESC	embryonic stem cell:	n/a	chr12:122020651-122020664
22	TEAD4	chr12:122020468-122021140	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZBTB7A	chr12:122020468-122020717	K562	blood:	n/a	n/a
24	SP4	chr12:122020413-122021026	H1-hESC	embryonic stem cell:	n/a	n/a
25	TEAD4	chr12:122020540-122020974	K562	blood:	n/a	n/a
26	TCF7L2	chr12:122020434-122021139	HepG2	liver:	n/a	chr12:122021067-122021083 chr12:122020752-122020761
27	FOS	chr12:122020462-122020997	HUVEC	blood vessel:	n/a	chr12:122020698-122020709
28	JUND	chr12:122020534-122020892	H1-hESC	embryonic stem cell:	n/a	chr12:122020698-122020709
29	GATA1	chr12:122018806-122020867	PBDE	blood:	n/a	chr12:122020736-122020753 chr12:122019496-122019505 chr12:122020731-122020747
30	JUND	chr12:122020299-122021187	H1-hESC	embryonic stem cell:	n/a	chr12:122020698-122020709
31	CEBPB	chr12:122020616-122021280	H1-hESC	embryonic stem cell:	n/a	n/a
32	TAF7	chr12:122019836-122021304	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr12:122019556-122021300	H1-hESC	embryonic stem cell:	n/a	chr12:122019709-122019717
34	CTBP2	chr12:122020413-122020947	H1-hESC	embryonic stem cell:	n/a	n/a
35	EGR1	chr12:122020560-122020902	K562	blood:	n/a	n/a
36	POLR2A	chr12:122020620-122020886	HUVEC	blood vessel:	n/a	n/a
37	EGR1	chr12:122020589-122020989	H1-hESC	embryonic stem cell:	n/a	n/a
38	TBL1XR1	chr12:122020580-122020909	K562	blood:	n/a	n/a
39	EP300	chr12:122020462-122020925	HepG2	liver:	n/a	chr12:122020724-122020738
40	SIN3AK20	chr12:122020607-122020958	H1-hESC	embryonic stem cell:	n/a	n/a
41	ZNF143	chr12:122020493-122020972	H1-hESC	embryonic stem cell:	n/a	n/a
42	SP1	chr12:122020342-122021157	H1-hESC	embryonic stem cell:	n/a	n/a
43	RCOR1	chr12:122020566-122020920	K562	blood:	n/a	n/a
44	CCNT2	chr12:122020634-122020798	K562	blood:	n/a	chr12:122020733-122020753
45	CUX1	chr12:122020518-122020918	K562	blood:	n/a	n/a
46	POLR2A	chr12:122020434-122021205	H1-hESC	embryonic stem cell:	n/a	n/a
47	SP1	chr12:122020399-122021095	H1-hESC	embryonic stem cell:	n/a	n/a
48	JUND	chr12:122020598-122020850	HepG2	liver:	n/a	chr12:122020698-122020709
49	POLR2A	chr12:122017817-122021420	H1-hESC	embryonic stem cell:	n/a	n/a
50	SIN3A	chr12:122017791-122021030	H1-hESC	embryonic stem cell:	n/a	chr12:122018963-122018974

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:122020661-122020711	ECC-1	luminal epithelium:	n/a
2	chr12:122020661-122020711	AoSMC	blood vessel:	n/a
3	chr12:122020661-122020711	GM12891	blood:	n/a
4	chr12:122020661-122020711	HNPCEpiC	eye:	n/a
5	chr12:122020661-122020711	HL-60	blood:	n/a
6	chr12:122020661-122020711	HCM	heart:	n/a
7	chr12:122020661-122020711	HPAEpiC	pulmonary alveolar:	n/a
8	chr12:122020661-122020711	U87	brain:	n/a
9	chr12:122020661-122020711	NH-A	brain:	n/a
10	chr12:122020661-122020711	GM06990	blood:	n/a
11	chr12:122020661-122020711	Hepatocyte	liver:	n/a
12	chr12:122020661-122020711	HIPEpiC	eye:	n/a
13	chr12:122020661-122020711	CMK	blood:	n/a
14	chr12:122020661-122020711	NB4	blood:	n/a
15	chr12:122020661-122020711	HCT-116	colon:	n/a
16	chr12:122020661-122020711	MCF10A-Er-Src	breast:	n/a
17	chr12:122020661-122020711	NHBE	bronchial:	n/a
18	chr12:122020661-122020711	LNCaP	prostate:	n/a
19	chr12:122020661-122020711	A549	lung:	n/a
20	chr12:122020661-122020711	IMR90	lung:	fetal
21	chr12:122020661-122020711	HRPEpiC	eye:	n/a
22	chr12:122020661-122020711	ProgFib	skin:	n/a
23	chr12:122020661-122020711	HEK293	kidney:	embryo
24	chr12:122020661-122020711	SK-N-SH	brain:	n/a
25	chr12:122020661-122020711	AG10803	skin:	n/a
26	chr12:122020661-122020711	AG09309	skin:	n/a
27	chr12:122020661-122020711	HMEC	breast:	n/a
28	chr12:122020661-122020711	T-47D	breast:	n/a
29	chr12:122020661-122020711	Jurkat	blood:	n/a
30	chr12:122020661-122020711	AG04449	skin:	fetal
31	chr12:122020661-122020711	GM19239	blood:	n/a
32	chr12:122020661-122020711	AG09319	gingival:	n/a
33	chr12:122020661-122020711	K562	blood:	n/a
34	chr12:122020661-122020711	GM12892	blood:	n/a
35	chr12:122020661-122020711	HEEpiC	esophagus:	n/a
36	chr12:122020661-122020711	SKMC	muscle:	n/a
37	chr12:122020661-122020711	PFSK-1	brain:	n/a
38	chr12:122020661-122020711	Hela-S3	cervix:	n/a
39	chr12:122020661-122020711	HAEpiC	amniotic membrane:	n/a
40	chr12:122020661-122020711	NT2-D1	testis:	n/a
41	chr12:122020661-122020711	MCF-7	breast:	n/a
42	chr12:122020661-122020711	HCPEpiC	choroid plexus:	n/a
43	chr12:122020661-122020711	SK-N-SH_RA	brain:	n/a
44	chr12:122020661-122020711	BE2_C	brain:	n/a
45	chr12:122020661-122020711	ovcar-3	ovarian:	n/a
46	chr12:122020661-122020711	GM12878	blood:	n/a
47	chr12:122020661-122020711	SK-N-MC	brain:	n/a
48	chr12:122020661-122020711	BJ	skin:	n/a
49	chr12:122020661-122020711	PrEC	prostate:	n/a
50	chr12:122020661-122020711	AG04450	lung:	fetal

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

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:

No data

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

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12313273	0.87[MEX][hapmap]
rs28378998	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28397246	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28435255	0.84[AMR][1000 genomes]
rs28508138	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28546504	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28594507	0.84[MEX][hapmap]
rs3741595	0.92[MEX][hapmap];0.81[TSI][hapmap]
rs6486795	0.87[MEX][hapmap]
rs7313601	0.95[MEX][hapmap]
rs73227906	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227912	0.83[AFR][1000 genomes];0.94[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28517331	GTF2H3	cis	cerebellum	SCAN
rs28517331	SRRM4	cis	cerebellum	SCAN
rs28517331	NME2P1	cis	cerebellum	SCAN

Chromatin state (count:108 , 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	chr12:122014800-122020800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr12:122014800-122021000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:122014800-122021000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:122015400-122021000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:122015600-122021800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:122015800-122021000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:122016000-122021000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:122017200-122021200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:122018400-122020800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:122018600-122020800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr12:122018600-122020800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr12:122018600-122020800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr12:122018600-122020800	Flanking Active TSS	Dnd41	blood
15	chr12:122018600-122020800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr12:122018600-122021000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:122018600-122021000	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr12:122018600-122021000	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr12:122018600-122021400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:122019000-122021200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:122019200-122020800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:122019200-122020800	Enhancers	Fetal Muscle Trunk	muscle
23	chr12:122019200-122020800	Enhancers	Left Ventricle	heart
24	chr12:122019200-122021000	Enhancers	Fetal Intestine Large	intestine
25	chr12:122019400-122021000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:122019400-122021000	Enhancers	Fetal Stomach	stomach
27	chr12:122019400-122021200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:122019600-122021000	Weak transcription	Pancreas	Pancrea
29	chr12:122019800-122021200	Enhancers	Fetal Thymus	thymus
30	chr12:122019800-122021800	Enhancers	A549	lung
31	chr12:122019800-122023000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr12:122020000-122020800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:122020000-122020800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:122020000-122020800	Enhancers	Fetal Brain Male	brain
35	chr12:122020000-122020800	Enhancers	HSMM	muscle
36	chr12:122020000-122021000	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr12:122020000-122021000	Weak transcription	Spleen	Spleen
38	chr12:122020000-122021200	Enhancers	Primary B cells from peripheral blood	blood
39	chr12:122020000-122021200	Enhancers	Fetal Muscle Leg	muscle
40	chr12:122020000-122021400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr12:122020000-122022000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr12:122020200-122020800	Enhancers	Primary B cells from cord blood	blood
43	chr12:122020200-122020800	Enhancers	Colon Smooth Muscle	Colon
44	chr12:122020200-122020800	Enhancers	Duodenum Mucosa	Duodenum
45	chr12:122020200-122020800	Enhancers	Psoas Muscle	Psoas
46	chr12:122020200-122020800	Enhancers	Right Atrium	heart
47	chr12:122020200-122020800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr12:122020200-122021000	Active TSS	H1 Cell Line	embryonic stem cell
49	chr12:122020200-122021000	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr12:122020200-122021000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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