Variant report

Variant	rs28498205
Chromosome Location	chr12:123851874-123851875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
2	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
3	chr12:123845591..123852236-chr12:123866929..123875043,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10082867	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	0.94[ASN][1000 genomes]
rs10773004	0.97[ASN][1000 genomes]
rs10773005	0.97[ASN][1000 genomes]
rs10773006	0.97[ASN][1000 genomes]
rs10773018	0.80[ASN][1000 genomes]
rs10846497	0.83[ASN][1000 genomes]
rs10846505	0.89[ASN][1000 genomes]
rs10846506	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	0.93[ASN][1000 genomes]
rs11057248	0.93[ASN][1000 genomes]
rs11057251	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057254	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057261	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057273	0.98[ASN][1000 genomes]
rs11057275	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11057276	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057283	0.81[ASN][1000 genomes]
rs11057284	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057287	0.81[ASN][1000 genomes]
rs11503021	0.94[ASN][1000 genomes]
rs11608297	0.87[ASN][1000 genomes]
rs11608305	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611141	0.98[ASN][1000 genomes]
rs11611677	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11611679	0.94[ASN][1000 genomes]
rs11611680	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11611694	0.98[ASN][1000 genomes]
rs11612234	0.81[ASN][1000 genomes]
rs12317103	0.98[ASN][1000 genomes]
rs12317452	0.97[ASN][1000 genomes]
rs12366872	0.98[ASN][1000 genomes]
rs12367421	0.95[ASN][1000 genomes]
rs12582153	0.95[ASN][1000 genomes]
rs13303208	0.91[ASN][1000 genomes]
rs28410096	0.97[ASN][1000 genomes]
rs28418709	0.81[ASN][1000 genomes]
rs28419092	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28450974	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28461471	0.97[ASN][1000 genomes]
rs28496545	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28503862	0.97[ASN][1000 genomes]
rs28516750	0.93[ASN][1000 genomes]
rs28517382	0.81[ASN][1000 genomes]
rs28532037	0.97[ASN][1000 genomes]
rs28533432	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28556815	0.86[ASN][1000 genomes]
rs28565984	0.83[ASN][1000 genomes]
rs28574664	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28577594	0.91[ASN][1000 genomes]
rs28581850	0.97[ASN][1000 genomes]
rs28592032	0.97[ASN][1000 genomes]
rs28594416	0.81[ASN][1000 genomes]
rs28631104	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28631903	0.81[ASN][1000 genomes]
rs28642812	0.91[ASN][1000 genomes]
rs28690326	0.85[ASN][1000 genomes]
rs28703745	0.80[ASN][1000 genomes]
rs28718696	0.80[ASN][1000 genomes]
rs28759130	0.81[ASN][1000 genomes]
rs28786830	0.97[ASN][1000 genomes]
rs28820735	0.97[ASN][1000 genomes]
rs28825193	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28866344	0.93[ASN][1000 genomes]
rs3088303	0.95[ASN][1000 genomes]
rs34032470	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35818434	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825141	0.81[ASN][1000 genomes]
rs4759375	0.97[ASN][1000 genomes]
rs4759376	0.81[ASN][1000 genomes]
rs4759377	0.98[ASN][1000 genomes]
rs4759421	0.81[ASN][1000 genomes]
rs56116847	0.98[ASN][1000 genomes]
rs56197170	0.85[ASN][1000 genomes]
rs56309603	0.89[ASN][1000 genomes]
rs57416942	0.81[ASN][1000 genomes]
rs59295450	0.81[ASN][1000 genomes]
rs60835840	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61388686	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61751327	0.81[ASN][1000 genomes]
rs61955125	0.89[ASN][1000 genomes]
rs6416290	0.86[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	0.98[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	0.98[ASN][1000 genomes]
rs7315453	0.98[ASN][1000 genomes]
rs73216931	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[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	0.98[ASN][1000 genomes]
rs7955367	0.81[ASN][1000 genomes]
rs7959415	0.81[ASN][1000 genomes]
rs7970080	0.81[ASN][1000 genomes]
rs7972811	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	0.98[ASN][1000 genomes]
rs9669295	0.98[ASN][1000 genomes]
rs9705407	0.94[ASN][1000 genomes]
rs9739171	0.98[ASN][1000 genomes]
rs9739565	0.81[ASN][1000 genomes]
rs9795593	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28498205	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28498205	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28498205	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28498205	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28498205	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28498205	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28498205	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123850400-123856200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:123850600-123852000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:123850600-123852200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:123850600-123852200	Weak transcription	A549	lung
5	chr12:123850600-123867200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:123850600-123867800	Weak transcription	Right Atrium	heart
7	chr12:123850800-123852000	Enhancers	Primary B cells from cord blood	blood
8	chr12:123850800-123852000	Weak transcription	Hela-S3	cervix
9	chr12:123850800-123856800	Weak transcription	HepG2	liver
10	chr12:123851200-123852200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:123851200-123853400	Weak transcription	K562	blood
12	chr12:123851200-123856200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:123851600-123853400	Weak transcription	GM12878-XiMat	blood

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