Variant report

Variant	rs28475177
Chromosome Location	chr12:123872037-123872038
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123871918-123873823	K562	blood:	n/a	n/a
2	ATF1	chr12:123872000-123873150	K562	blood:	n/a	n/a
3	IRF1	chr12:123871853-123873232	K562	blood:	n/a	chr12:123872050-123872063 chr12:123872050-123872064 chr12:123872050-123872061
4	ZNF274	chr12:123871829-123873085	K562	blood:	n/a	n/a
5	TEAD4	chr12:123871696-123873389	K562	blood:	n/a	n/a
6	CEBPD	chr12:123871766-123873277	K562	blood:	n/a	n/a
7	TAL1	chr12:123871943-123873222	K562	blood:	n/a	n/a
8	STAT5A	chr12:123872016-123873279	K562	blood:	n/a	n/a
9	POLR2A	chr12:123871919-123873387	K562	blood:	n/a	n/a
10	RCOR1	chr12:123871928-123873269	K562	blood:	n/a	n/a
11	GATA1	chr12:123871860-123873276	PBDE	blood:	n/a	chr12:123872319-123872328 chr12:123872318-123872328 chr12:123872319-123872328
12	HDAC2	chr12:123871999-123873129	K562	blood:	n/a	chr12:123872318-123872327
13	POLR2A	chr12:123871971-123875084	K562	blood:	n/a	n/a
14	NR2F2	chr12:123871915-123873215	K562	blood:	n/a	n/a
15	GATA1	chr12:123871817-123873266	K562	blood:	n/a	chr12:123872319-123872328 chr12:123872318-123872328 chr12:123872319-123872328
16	NR2F2	chr12:123871720-123873354	K562	blood:	n/a	n/a
17	TBL1XR1	chr12:123871978-123873233	K562	blood:	n/a	n/a
18	GATA2	chr12:123871921-123873203	K562	blood:	n/a	chr12:123872319-123872328 chr12:123872318-123872328 chr12:123872319-123872328
19	POLR2A	chr12:123871970-123873293	K562	blood:	n/a	n/a
20	BHLHE40	chr12:123871961-123873162	K562	blood:	n/a	n/a
21	RCOR1	chr12:123872006-123873273	K562	blood:	n/a	n/a
22	JUND	chr12:123871839-123873269	K562	blood:	n/a	n/a
23	POLR2A	chr12:123872033-123873203	K562	blood:	n/a	n/a
24	TBL1XR1	chr12:123871943-123873169	K562	blood:	n/a	n/a
25	CEBPD	chr12:123872026-123873173	K562	blood:	n/a	n/a
26	MAX	chr12:123871864-123873265	K562	blood:	n/a	n/a
27	IRF1	chr12:123871967-123873254	K562	blood:	n/a	chr12:123872050-123872063 chr12:123872050-123872064 chr12:123872050-123872061
28	PML	chr12:123872007-123873236	K562	blood:	n/a	n/a
29	TBP	chr12:123871979-123873242	K562	blood:	n/a	n/a
30	STAT5A	chr12:123872017-123872467	K562	blood:	n/a	n/a
31	TEAD4	chr12:123871925-123873267	K562	blood:	n/a	n/a
32	JUN	chr12:123871997-123873119	K562	blood:	n/a	n/a
33	POLR2A	chr12:123871624-123873557	K562	blood:	n/a	n/a
34	EP300	chr12:123872035-123873197	K562	blood:	n/a	n/a
35	CUX1	chr12:123871829-123873142	K562	blood:	n/a	n/a
36	MYC	chr12:123871799-123873240	K562	blood:	n/a	n/a
37	TRIM28	chr12:123872029-123873325	K562	blood:	n/a	n/a
38	POLR2A	chr12:123872004-123873615	K562	blood:	n/a	n/a
39	PML	chr12:123871865-123873289	K562	blood:	n/a	n/a
40	CBX3	chr12:123871927-123873272	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123717467..123721119-chr12:123869942..123873013,3	K562	blood:
2	chr12:123845591..123852236-chr12:123866929..123875043,19	MCF-7	breast:
3	chr12:123715746..123718967-chr12:123870796..123875270,4	K562	blood:
4	chr12:123755164..123758333-chr12:123868507..123873426,5	K562	blood:
5	chr12:123458609..123460830-chr12:123870435..123872750,2	K562	blood:
6	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
7	chr12:123871392..123873266-chr12:123879118..123880787,2	K562	blood:
8	chr12:123871385..123875741-chr12:124017374..124019532,6	MCF-7	breast:
9	chr12:123753478..123757222-chr12:123871925..123875006,5	K562	blood:
10	chr12:123870684..123873491-chr12:123941342..123943069,2	MCF-7	breast:
11	chr12:123754759..123757395-chr12:123866766..123872450,7	MCF-7	breast:
12	chr12:123753572..123756952-chr12:123872035..123874712,3	MCF-7	breast:
13	chr12:123871220..123873431-chr12:123897619..123900288,2	K562	blood:
14	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
15	chr12:123870366..123875219-chr12:124064500..124069174,6	K562	blood:

No data

Variant related genes	Relation type
SETD8	TF binding region
ENSG00000111328	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000256028	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10083067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs10444447	0.82[ASN][1000 genomes]
rs10444448	0.82[ASN][1000 genomes]
rs10773003	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs10773005	0.82[GIH][hapmap];0.85[YRI][hapmap]
rs10773007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10773009	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773010	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846495	0.82[ASN][1000 genomes]
rs10846496	0.82[ASN][1000 genomes]
rs10846498	0.82[ASN][1000 genomes]
rs10846499	0.82[ASN][1000 genomes]
rs10846500	0.82[ASN][1000 genomes]
rs10846501	0.82[ASN][1000 genomes]
rs10846503	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10846504	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10846509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10846510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846511	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846513	0.85[MEX][hapmap]
rs10846514	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846521	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846522	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846524	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057223	1.00[YRI][hapmap]
rs11057231	0.82[ASN][1000 genomes]
rs11057240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11057243	0.91[ASN][1000 genomes]
rs11057250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11057264	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057273	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs11057285	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057286	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317452	1.00[YRI][hapmap]
rs12366872	1.00[YRI][hapmap]
rs12371973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1402275	0.85[YRI][hapmap]
rs1662	0.82[CHB][hapmap]
rs28376696	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28377694	1.00[ASN][1000 genomes]
rs28397122	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28410096	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs28454135	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532037	0.82[GIH][hapmap]
rs28573826	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28633324	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28646185	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28655516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660661	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660993	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs28713448	0.82[CHB][hapmap]
rs28861152	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898283	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088303	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs4281511	0.91[ASN][1000 genomes]
rs4313613	0.91[ASN][1000 genomes]
rs4759375	1.00[YRI][hapmap]
rs4759377	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs61953413	0.82[ASN][1000 genomes]
rs61955088	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61955089	0.91[ASN][1000 genomes]
rs61955114	0.91[ASN][1000 genomes]
rs61955117	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488868	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7315453	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs73231946	0.82[ASN][1000 genomes]
rs7972811	0.82[GIH][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv826534	chr12:123859610-123876354	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28475177	CDK2AP1	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123869600-123872200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:123869600-123872200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:123869600-123872200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:123869600-123872200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:123869600-123872200	Weak transcription	Adipose Nuclei	Adipose
6	chr12:123869600-123872200	Weak transcription	Brain Substantia Nigra	brain
7	chr12:123869600-123872200	Weak transcription	Fetal Brain Male	brain
8	chr12:123869600-123872200	Weak transcription	Placenta	Placenta
9	chr12:123869600-123872200	Weak transcription	Gastric	stomach
10	chr12:123869600-123872200	Weak transcription	Lung	lung
11	chr12:123869600-123872200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:123869600-123872200	Weak transcription	Right Atrium	heart
13	chr12:123869600-123872200	Weak transcription	Right Ventricle	heart
14	chr12:123869600-123872200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:123869600-123872200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:123869600-123872200	Weak transcription	HSMMtube	muscle
17	chr12:123869600-123872400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:123869600-123872400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:123869600-123872400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:123869600-123872400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:123869600-123872400	Weak transcription	Brain Angular Gyrus	brain
22	chr12:123869600-123872400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:123869600-123872400	Weak transcription	Brain Germinal Matrix	brain
24	chr12:123869600-123872400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:123869600-123872400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:123869600-123872400	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:123869600-123872400	Enhancers	Fetal Intestine Small	intestine
28	chr12:123869600-123872600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:123869600-123872600	Weak transcription	Ovary	ovary
30	chr12:123869600-123872600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:123869600-123872600	Weak transcription	Small Intestine	intestine
32	chr12:123869600-123873000	Weak transcription	Aorta	Aorta
33	chr12:123869800-123872200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:123869800-123872200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr12:123869800-123872200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:123869800-123872200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr12:123869800-123872200	Weak transcription	Liver	Liver
38	chr12:123869800-123872200	Weak transcription	Colonic Mucosa	Colon
39	chr12:123869800-123872200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:123869800-123872200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:123869800-123872200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr12:123869800-123872200	Weak transcription	Thymus	Thymus
43	chr12:123869800-123872200	Enhancers	Hela-S3	cervix
44	chr12:123869800-123872400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:123869800-123872400	Weak transcription	Fetal Brain Female	brain
46	chr12:123869800-123872400	Weak transcription	Fetal Kidney	kidney
47	chr12:123869800-123872400	Weak transcription	Fetal Lung	lung
48	chr12:123869800-123872400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:123869800-123872800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr12:123870000-123872200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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