Variant report

Variant	rs28516750
Chromosome Location	chr12:123867994-123867995
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	POLR2A	chr12:123867926-123868957	HepG2	liver:	n/a	n/a
2	ELF1	chr12:123867978-123869095	GM12878	blood:	n/a	chr12:123868306-123868317 chr12:123868307-123868316
3	POLR2A	chr12:123867829-123869579	U87	brain:	n/a	n/a
4	MBD4	chr12:123867990-123868365	HepG2	liver:	n/a	n/a
5	HEY1	chr12:123867936-123868488	HepG2	liver:	n/a	n/a
6	SIN3AK20	chr12:123867900-123869663	MCF-7	breast:	n/a	n/a
7	POLR2A	chr12:123867860-123868913	K562	blood:	n/a	n/a
8	TCF12	chr12:123867819-123869665	A549	lung:	n/a	n/a
9	GATA3	chr12:123867942-123869086	A549	lung:	n/a	n/a
10	POLR2A	chr12:123867734-123869614	K562	blood:	n/a	n/a
11	POLR2A	chr12:123867878-123868939	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr12:123867804-123869579	U87	brain:	n/a	n/a
13	POLR2A	chr12:123867942-123868375	ECC-1	luminal epithelium:	n/a	n/a
14	SIX5	chr12:123867872-123868607	A549	lung:	n/a	n/a
15	EP300	chr12:123867929-123868739	A549	lung:	n/a	chr12:123868309-123868316
16	REST	chr12:123867905-123868920	A549	lung:	n/a	n/a
17	RUNX3	chr12:123867966-123869120	GM12878	blood:	n/a	n/a
18	BCL3	chr12:123867985-123868609	A549	lung:	n/a	n/a
19	TAF1	chr12:123867956-123868907	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:123867919-123868432	HepG2	liver:	n/a	n/a
21	NR2F2	chr12:123867960-123868623	MCF-7	breast:	n/a	chr12:123868269-123868284
22	HCFC1	chr12:123867831-123870047	Hela-S3	cervix:	n/a	n/a
23	SIN3AK20	chr12:123867970-123869237	MCF-7	breast:	n/a	n/a
24	MXI1	chr12:123867987-123869474	HepG2	liver:	n/a	n/a
25	MAX	chr12:123867848-123869541	A549	lung:	n/a	chr12:123868621-123868631 chr12:123868882-123868891
26	POLR2A	chr12:123867926-123868927	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr12:123867943-123868506	GM12892	blood:	n/a	n/a
28	NR2F2	chr12:123867968-123868981	MCF-7	breast:	n/a	chr12:123868269-123868284
29	REST	chr12:123867842-123868688	H1-neurons	neurons:	n/a	n/a
30	FOSL2	chr12:123867934-123869233	A549	lung:	n/a	chr12:123868918-123868927
31	SP1	chr12:123867849-123869107	HCT-116	colon:	n/a	chr12:123868390-123868404 chr12:123868569-123868581 chr12:123869094-123869107 chr12:123868558-123868569 chr12:123868483-123868497 chr12:123868571-123868580 chr12:123868569-123868581 chr12:123868479-123868489 chr12:123868566-123868580 chr12:123868569-123868580
32	MAZ	chr12:123867950-123869825	IMR90	lung:	n/a	chr12:123868621-123868631 chr12:123869757-123869766 chr12:123868882-123868891
33	POLR2A	chr12:123867983-123869545	K562	blood:	n/a	n/a
34	PML	chr12:123867919-123869016	K562	blood:	n/a	n/a
35	MXI1	chr12:123867946-123869830	IMR90	lung:	n/a	n/a
36	SP1	chr12:123867866-123869657	HCT-116	colon:	n/a	chr12:123868390-123868404 chr12:123868569-123868581 chr12:123869099-123869108 chr12:123869094-123869107 chr12:123868558-123868569 chr12:123869407-123869420 chr12:123868483-123868497 chr12:123868571-123868580 chr12:123869098-123869110 chr12:123869098-123869110 chr12:123868569-123868581 chr12:123868479-123868489 chr12:123868566-123868580 chr12:123868569-123868580 chr12:123869100-123869109
37	POLR2A	chr12:123867929-123868411	MCF-7	breast:	n/a	n/a
38	POLR2A	chr12:123867936-123869158	HCT-116	colon:	n/a	n/a
39	POLR2A	chr12:123867886-123868519	GM12892	blood:	n/a	n/a
40	POLR2A	chr12:123867988-123869553	K562	blood:	n/a	n/a
41	RXRA	chr12:123867947-123868607	SK-N-SH	brain:	n/a	chr12:123868271-123868284 chr12:123868266-123868282 chr12:123868268-123868288 chr12:123868271-123868284 chr12:123868270-123868286 chr12:123868271-123868284
42	POLR2A	chr12:123867792-123869551	K562	blood:	n/a	n/a
43	GTF3C2	chr12:123867869-123868250	Hela-S3	cervix:	n/a	n/a
44	POU2F2	chr12:123867891-123868920	GM12878	blood:	n/a	chr12:123868888-123868900 chr12:123868481-123868493
45	POLR2A	chr12:123867985-123868560	ECC-1	luminal epithelium:	n/a	n/a
46	TBP	chr12:123867994-123868957	K562	blood:	n/a	n/a
47	MYBL2	chr12:123867864-123868933	HepG2	liver:	n/a	n/a
48	MAX	chr12:123867947-123869373	ECC-1	luminal epithelium:	n/a	chr12:123868621-123868631 chr12:123868882-123868891
49	SP1	chr12:123867874-123869277	A549	lung:	n/a	chr12:123868390-123868404 chr12:123868569-123868581 chr12:123869099-123869108 chr12:123869094-123869107 chr12:123868558-123868569 chr12:123868483-123868497 chr12:123868571-123868580 chr12:123869098-123869110 chr12:123869098-123869110 chr12:123868569-123868581 chr12:123868479-123868489 chr12:123868566-123868580 chr12:123868569-123868580 chr12:123869100-123869109
50	TAF1	chr12:123867955-123868944	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123866701..123869300-chr12:124085669..124087764,2	K562	blood:
2	chr12:123845591..123852236-chr12:123866929..123875043,19	MCF-7	breast:
3	chr12:123867374..123868909-chr12:124067489..124069464,2	K562	blood:
4	chr12:123866820..123869752-chr12:123919792..123923261,3	K562	blood:
5	chr12:123755389..123758333-chr12:123866833..123870129,4	K562	blood:
6	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
7	chr12:123866977..123869044-chr12:124085781..124087608,2	MCF-7	breast:
8	chr12:123846880..123851536-chr12:123865445..123870876,12	MCF-7	breast:
9	chr12:123754759..123757395-chr12:123866766..123872450,7	MCF-7	breast:
10	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
11	chr12:123855413..123857472-chr12:123866745..123868291,2	K562	blood:
12	chr12:123866599..123869577-chr12:123942434..123944403,3	MCF-7	breast:
13	chr12:123867386..123869300-chr12:124085669..124087822,2	K562	blood:

Variant related genes	Relation type
SETD8	TF binding region
ENSG00000111328	Chromatin interaction
ENSG00000150977	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000184209	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10082867	0.94[ASN][1000 genomes]
rs10444439	0.83[ASN][1000 genomes]
rs10773003	0.90[ASN][1000 genomes]
rs10773004	0.93[ASN][1000 genomes]
rs10773005	0.93[ASN][1000 genomes]
rs10773006	0.93[ASN][1000 genomes]
rs10846505	0.86[ASN][1000 genomes]
rs10846506	0.91[ASN][1000 genomes]
rs11057238	0.81[ASN][1000 genomes]
rs11057242	0.89[ASN][1000 genomes]
rs11057248	0.90[ASN][1000 genomes]
rs11057251	0.93[ASN][1000 genomes]
rs11057254	0.94[ASN][1000 genomes]
rs11057261	0.94[ASN][1000 genomes]
rs11057273	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11057275	0.91[ASN][1000 genomes]
rs11057276	0.94[ASN][1000 genomes]
rs11057284	0.94[ASN][1000 genomes]
rs11503021	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11608297	0.83[ASN][1000 genomes]
rs11608305	0.93[ASN][1000 genomes]
rs11611141	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11611677	0.92[ASN][1000 genomes]
rs11611679	0.90[ASN][1000 genomes]
rs11611680	0.90[ASN][1000 genomes]
rs11611694	0.94[ASN][1000 genomes]
rs12317103	0.94[ASN][1000 genomes]
rs12317452	0.93[ASN][1000 genomes]
rs12366872	0.94[ASN][1000 genomes]
rs12367421	0.91[ASN][1000 genomes]
rs12582153	0.91[ASN][1000 genomes]
rs13303208	0.90[ASN][1000 genomes]
rs28410096	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28419092	0.94[ASN][1000 genomes]
rs28450974	0.96[ASN][1000 genomes]
rs28461471	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28496545	0.90[ASN][1000 genomes]
rs28498205	0.93[ASN][1000 genomes]
rs28503862	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28532037	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28533432	0.96[ASN][1000 genomes]
rs28556815	0.85[ASN][1000 genomes]
rs28565984	0.84[ASN][1000 genomes]
rs28574664	0.80[ASN][1000 genomes]
rs28577594	0.90[ASN][1000 genomes]
rs28581850	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28592032	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28631104	0.87[ASN][1000 genomes]
rs28642812	0.90[ASN][1000 genomes]
rs28690326	0.85[ASN][1000 genomes]
rs28786830	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28820735	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28825193	0.96[ASN][1000 genomes]
rs28866344	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3088303	0.91[ASN][1000 genomes]
rs34032470	0.86[ASN][1000 genomes]
rs35818434	0.93[ASN][1000 genomes]
rs4759375	0.93[ASN][1000 genomes]
rs4759377	0.94[ASN][1000 genomes]
rs56116847	0.94[ASN][1000 genomes]
rs56197170	0.81[ASN][1000 genomes]
rs56309603	0.88[ASN][1000 genomes]
rs60835840	0.94[ASN][1000 genomes]
rs61388686	0.94[ASN][1000 genomes]
rs61955125	0.88[ASN][1000 genomes]
rs6416290	0.82[ASN][1000 genomes]
rs6488873	0.85[ASN][1000 genomes]
rs7298909	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7312145	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7315453	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73216931	0.91[ASN][1000 genomes]
rs73231950	0.91[ASN][1000 genomes]
rs7954704	0.94[ASN][1000 genomes]
rs7972811	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7974099	0.83[ASN][1000 genomes]
rs9669273	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9669295	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9705407	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9739171	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28516750	CDK2AP1	cis	Whole Blood	GTEx
rs28516750	RP11-282O18.3	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123864600-123868000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:123867000-123868000	Enhancers	GM12878-XiMat	blood
3	chr12:123867000-123869600	Active TSS	HSMM	muscle
4	chr12:123867200-123868600	Enhancers	Spleen	Spleen
5	chr12:123867200-123868800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:123867200-123868800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:123867200-123869000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:123867200-123869000	Active TSS	Colonic Mucosa	Colon
9	chr12:123867200-123869400	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr12:123867200-123869400	Active TSS	A549	lung
11	chr12:123867200-123869600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:123867200-123869600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:123867200-123869800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr12:123867200-123870000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:123867400-123868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:123867400-123869000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:123867400-123869600	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:123867400-123869800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr12:123867400-123869800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:123867400-123870000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr12:123867400-123870000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:123867600-123868000	Flanking Active TSS	Placenta	Placenta
23	chr12:123867600-123868400	Flanking Active TSS	Fetal Muscle Trunk	muscle
24	chr12:123867600-123868800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:123867600-123869200	Active TSS	Fetal Intestine Large	intestine
26	chr12:123867600-123869200	Active TSS	Fetal Intestine Small	intestine
27	chr12:123867600-123869800	Active TSS	Hela-S3	cervix
28	chr12:123867600-123869800	Active TSS	HepG2	liver
29	chr12:123867600-123870200	Active TSS	K562	blood
30	chr12:123867800-123868000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:123867800-123868000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:123867800-123868000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr12:123867800-123868000	Enhancers	Primary B cells from cord blood	blood
34	chr12:123867800-123868000	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:123867800-123868000	Enhancers	Primary T cells fromperipheralblood	blood
36	chr12:123867800-123868000	Enhancers	Primary hematopoietic stem cells	blood
37	chr12:123867800-123868000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr12:123867800-123868000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:123867800-123868000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr12:123867800-123868000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:123867800-123868000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:123867800-123868000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:123867800-123868000	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr12:123867800-123868000	Enhancers	Fetal Thymus	thymus
45	chr12:123867800-123868000	Enhancers	Ovary	ovary
46	chr12:123867800-123868000	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr12:123867800-123868000	Active TSS	Rectal Smooth Muscle	rectum
48	chr12:123867800-123868000	Active TSS	Stomach Smooth Muscle	stomach
49	chr12:123867800-123868000	Enhancers	HUVEC	blood vessel
50	chr12:123867800-123868000	Active TSS	Monocytes-CD14+_RO01746	blood

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