Variant report

Variant	rs28503862
Chromosome Location	chr12:123867106-123867107
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123867028-123867564	K562	blood:	n/a	n/a
2	CUX1	chr12:123867102-123867366	K562	blood:	n/a	n/a
3	POLR2A	chr12:123867089-123867526	K562	blood:	n/a	n/a
4	CBX3	chr12:123867074-123867622	K562	blood:	n/a	n/a
5	TBL1XR1	chr12:123867060-123867327	K562	blood:	n/a	n/a
6	HEY1	chr12:123867056-123867608	K562	blood:	n/a	n/a
7	POLR2A	chr12:123866838-123867490	K562	blood:	n/a	n/a
8	POLR2A	chr12:123867034-123867544	K562	blood:	n/a	n/a
9	POLR2A	chr12:123867015-123867695	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

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	chr12:123866820..123869752-chr12:123919792..123923261,3	K562	blood:
4	chr12:123755389..123758333-chr12:123866833..123870129,4	K562	blood:
5	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
6	chr12:123866977..123869044-chr12:124085781..124087608,2	MCF-7	breast:
7	chr12:123846880..123851536-chr12:123865445..123870876,12	MCF-7	breast:
8	chr12:123754759..123757395-chr12:123866766..123872450,7	MCF-7	breast:
9	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
10	chr12:123855413..123857472-chr12:123866745..123868291,2	K562	blood:
11	chr12:123866599..123869577-chr12:123942434..123944403,3	MCF-7	breast:

No data

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

Extended variants
information (count: 151 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10082867	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10444439	0.86[ASN][1000 genomes]
rs10444449	0.83[ASN][1000 genomes]
rs10744152	0.81[ASN][1000 genomes]
rs10744153	0.81[ASN][1000 genomes]
rs10744154	0.81[ASN][1000 genomes]
rs10773003	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10773004	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10773005	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10773006	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10773018	0.80[ASN][1000 genomes]
rs10846497	0.83[ASN][1000 genomes]
rs10846505	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10846506	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10846517	0.81[ASN][1000 genomes]
rs10846519	0.81[ASN][1000 genomes]
rs10846523	0.81[ASN][1000 genomes]
rs11057238	0.85[ASN][1000 genomes]
rs11057242	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11057248	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11057251	0.97[ASN][1000 genomes]
rs11057254	0.98[ASN][1000 genomes]
rs11057261	0.98[ASN][1000 genomes]
rs11057273	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057275	0.95[ASN][1000 genomes]
rs11057276	0.98[ASN][1000 genomes]
rs11057283	0.81[ASN][1000 genomes]
rs11057284	0.98[ASN][1000 genomes]
rs11057287	0.81[ASN][1000 genomes]
rs11503021	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11608297	0.87[ASN][1000 genomes]
rs11608305	0.97[ASN][1000 genomes]
rs11611141	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11611677	0.96[ASN][1000 genomes]
rs11611679	0.94[ASN][1000 genomes]
rs11611680	0.94[ASN][1000 genomes]
rs11611694	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11612234	0.81[ASN][1000 genomes]
rs12317103	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12317452	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12366872	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12367421	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12582153	0.95[ASN][1000 genomes]
rs13303208	0.94[ASN][1000 genomes]
rs28410096	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28414347	0.83[ASN][1000 genomes]
rs28417583	0.83[ASN][1000 genomes]
rs28418709	0.81[ASN][1000 genomes]
rs28419092	0.98[ASN][1000 genomes]
rs28450974	1.00[ASN][1000 genomes]
rs28461471	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28496545	0.93[ASN][1000 genomes]
rs28498205	0.97[ASN][1000 genomes]
rs28501453	0.83[ASN][1000 genomes]
rs28516750	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28517382	0.81[ASN][1000 genomes]
rs28532037	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28533432	1.00[ASN][1000 genomes]
rs28537583	0.83[ASN][1000 genomes]
rs28546238	0.83[ASN][1000 genomes]
rs28556815	0.89[ASN][1000 genomes]
rs28565984	0.86[ASN][1000 genomes]
rs28574664	0.84[ASN][1000 genomes]
rs28577594	0.94[ASN][1000 genomes]
rs28581850	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587386	0.83[ASN][1000 genomes]
rs28592032	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594416	0.81[ASN][1000 genomes]
rs28595660	0.83[ASN][1000 genomes]
rs28602967	0.83[ASN][1000 genomes]
rs28611282	0.83[ASN][1000 genomes]
rs28613486	0.83[ASN][1000 genomes]
rs28631104	0.91[ASN][1000 genomes]
rs28631903	0.81[ASN][1000 genomes]
rs28642812	0.94[ASN][1000 genomes]
rs28681105	0.83[ASN][1000 genomes]
rs28690326	0.88[ASN][1000 genomes]
rs28703745	0.80[ASN][1000 genomes]
rs28718696	0.80[ASN][1000 genomes]
rs28759130	0.81[ASN][1000 genomes]
rs28786830	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28820735	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28825193	1.00[ASN][1000 genomes]
rs28865692	0.82[ASN][1000 genomes]
rs28866344	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28885203	0.82[ASN][1000 genomes]
rs28886709	0.81[ASN][1000 genomes]
rs3088303	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34032470	0.90[ASN][1000 genomes]
rs35818434	0.97[ASN][1000 genomes]
rs3825141	0.81[ASN][1000 genomes]
rs4759375	0.97[ASN][1000 genomes]
rs4759376	0.81[ASN][1000 genomes]
rs4759377	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759421	0.81[ASN][1000 genomes]
rs56116847	0.98[ASN][1000 genomes]
rs56197170	0.85[ASN][1000 genomes]
rs56309603	0.92[ASN][1000 genomes]
rs57416942	0.81[ASN][1000 genomes]
rs59295450	0.81[ASN][1000 genomes]
rs60835840	0.98[ASN][1000 genomes]
rs61388686	0.98[ASN][1000 genomes]
rs61751327	0.81[ASN][1000 genomes]
rs61955125	0.92[ASN][1000 genomes]
rs6416290	0.85[ASN][1000 genomes]
rs6488869	0.81[ASN][1000 genomes]
rs6488870	0.81[ASN][1000 genomes]
rs6488871	0.81[ASN][1000 genomes]
rs6488872	0.81[ASN][1000 genomes]
rs6488873	0.89[ASN][1000 genomes]
rs7137243	0.81[ASN][1000 genomes]
rs7297649	0.81[ASN][1000 genomes]
rs7298909	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7301163	0.81[ASN][1000 genomes]
rs7303754	0.82[ASN][1000 genomes]
rs7310756	0.81[ASN][1000 genomes]
rs7311304	0.81[ASN][1000 genomes]
rs7312145	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7315453	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73216931	0.95[ASN][1000 genomes]
rs73231950	0.95[ASN][1000 genomes]
rs7484644	0.81[ASN][1000 genomes]
rs7485967	0.81[ASN][1000 genomes]
rs7486223	0.81[ASN][1000 genomes]
rs7488340	0.81[ASN][1000 genomes]
rs7488490	0.80[ASN][1000 genomes]
rs7952835	0.81[ASN][1000 genomes]
rs7954704	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7955367	0.81[ASN][1000 genomes]
rs7959415	0.81[ASN][1000 genomes]
rs7970080	0.81[ASN][1000 genomes]
rs7972811	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973131	0.81[ASN][1000 genomes]
rs7973878	0.81[ASN][1000 genomes]
rs7974099	0.87[ASN][1000 genomes]
rs7977563	0.81[ASN][1000 genomes]
rs9284166	0.81[ASN][1000 genomes]
rs9300257	0.81[ASN][1000 genomes]
rs9300259	0.80[ASN][1000 genomes]
rs9669169	0.81[ASN][1000 genomes]
rs9669273	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9669295	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9705407	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9739171	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9739565	0.81[ASN][1000 genomes]
rs9795593	0.81[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
rs28503862	RP11-282O18.3	cis	Whole Blood	GTEx
rs28503862	CDK2AP1	cis	Whole Blood	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123850600-123867200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:123850600-123867800	Weak transcription	Right Atrium	heart
3	chr12:123859200-123867200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:123864000-123867200	Weak transcription	Placenta	Placenta
5	chr12:123864200-123867200	Weak transcription	A549	lung
6	chr12:123864200-123867400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:123864400-123867200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:123864400-123867800	Weak transcription	HMEC	breast
9	chr12:123864400-123867800	Weak transcription	NHEK	skin
10	chr12:123864600-123868000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:123865600-123867200	Weak transcription	Psoas Muscle	Psoas
12	chr12:123866800-123867200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:123866800-123867200	Enhancers	HepG2	liver
14	chr12:123867000-123867200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr12:123867000-123867200	Enhancers	Hela-S3	cervix
16	chr12:123867000-123867600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:123867000-123867600	Flanking Active TSS	K562	blood
18	chr12:123867000-123868000	Enhancers	GM12878-XiMat	blood
19	chr12:123867000-123869600	Active TSS	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links