Variant report

Variant	rs28532037
Chromosome Location	chr12:123883406-123883407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123881385..123883627-chr12:123929394..123932361,2	MCF-7	breast:
2	chr12:123881479..123883562-chr12:123887318..123890802,3	MCF-7	breast:
3	chr12:123882533..123885309-chr12:123899138..123901801,2	MCF-7	breast:
4	chr12:123879767..123882314-chr12:123882742..123884960,2	MCF-7	breast:
5	chr12:123883208..123885553-chr12:123941974..123944091,2	MCF-7	breast:
6	chr12:123847504..123849899-chr12:123882139..123884524,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139697	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000256092	Chromatin interaction

Extended variants
information (count: 172 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10082867	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10444439	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10444449	0.83[ASN][1000 genomes]
rs10744151	0.80[JPT][hapmap]
rs10744152	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10744153	0.81[ASN][1000 genomes]
rs10744154	0.81[ASN][1000 genomes]
rs10772997	0.84[JPT][hapmap]
rs10773000	0.94[JPT][hapmap]
rs10773003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs10773004	0.97[ASN][1000 genomes]
rs10773005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[ASN][1000 genomes]
rs10773006	0.97[ASN][1000 genomes]
rs10773007	0.82[GIH][hapmap]
rs10773018	0.80[ASN][1000 genomes]
rs10846489	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs10846497	0.83[ASN][1000 genomes]
rs10846505	0.89[ASN][1000 genomes]
rs10846506	0.95[ASN][1000 genomes]
rs10846509	0.82[GIH][hapmap]
rs10846514	0.82[GIH][hapmap]
rs10846517	0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10846518	0.82[GIH][hapmap]
rs10846519	0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10846523	0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11057223	1.00[CEU][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap]
rs11057238	0.85[ASN][1000 genomes]
rs11057242	0.93[ASN][1000 genomes]
rs11057248	0.93[ASN][1000 genomes]
rs11057251	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11057254	0.98[ASN][1000 genomes]
rs11057261	0.98[ASN][1000 genomes]
rs11057266	0.82[GIH][hapmap]
rs11057273	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057275	0.95[ASN][1000 genomes]
rs11057276	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11057283	0.81[ASN][1000 genomes]
rs11057284	0.98[ASN][1000 genomes]
rs11057287	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1109559	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs1109560	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs11503021	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11608297	0.87[ASN][1000 genomes]
rs11608305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11611141	0.90[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	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11612234	0.81[ASN][1000 genomes]
rs12317103	0.98[ASN][1000 genomes]
rs12317452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12366872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12367421	0.95[ASN][1000 genomes]
rs12582153	0.95[ASN][1000 genomes]
rs13303208	0.94[ASN][1000 genomes]
rs1568428	0.94[JPT][hapmap]
rs1790104	0.85[JPT][hapmap]
rs1879379	0.94[JPT][hapmap]
rs2271976	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs28410096	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[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28414347	0.94[CHD][hapmap];0.84[JPT][hapmap];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	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28475177	0.82[GIH][hapmap]
rs28496545	0.93[ASN][1000 genomes]
rs28498205	0.97[ASN][1000 genomes]
rs28501453	0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs28503862	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28516750	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28517382	0.81[ASN][1000 genomes]
rs28533432	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];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[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587386	0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs28592032	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594416	0.81[ASN][1000 genomes]
rs28595660	0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs28602967	0.83[ASN][1000 genomes]
rs28611282	0.83[ASN][1000 genomes]
rs28613486	0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs28631104	0.91[ASN][1000 genomes]
rs28631903	0.81[ASN][1000 genomes]
rs28642812	0.94[ASN][1000 genomes]
rs28655516	0.82[GIH][hapmap]
rs28660993	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[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
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	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28820735	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28825193	1.00[ASN][1000 genomes]
rs28865692	0.82[ASN][1000 genomes]
rs28866344	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28885203	0.82[ASN][1000 genomes]
rs28886709	0.81[ASN][1000 genomes]
rs3088303	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[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[ASN][1000 genomes]
rs34032470	0.90[ASN][1000 genomes]
rs35818434	0.97[ASN][1000 genomes]
rs3803001	0.94[CHD][hapmap];0.84[JPT][hapmap]
rs3825141	0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4759375	0.97[ASN][1000 genomes]
rs4759376	0.81[ASN][1000 genomes]
rs4759377	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[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]
rs7139321	0.94[JPT][hapmap]
rs7297649	0.94[CHD][hapmap];0.84[JPT][hapmap];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	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7315453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[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	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7955367	0.81[ASN][1000 genomes]
rs7959415	0.94[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs7970080	0.81[ASN][1000 genomes]
rs7972811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[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	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9669295	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9705407	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9739171	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9739565	0.81[ASN][1000 genomes]
rs9795593	0.94[CHD][hapmap];0.83[JPT][hapmap];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	esv3390938	chr12:123883379-123883696	Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28532037	CDK2AP1	cis	Whole Blood	GTEx
rs28532037	RP11-282O18.3	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875000-123884400	Strong transcription	Thymus	Thymus
2	chr12:123875000-123886400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123875200-123884400	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr12:123875200-123884600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:123875200-123894400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:123875400-123883600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:123875400-123884600	Strong transcription	Primary T cells from cord blood	blood
8	chr12:123875600-123884000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:123875600-123884200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:123875600-123884200	Strong transcription	A549	lung
11	chr12:123875600-123884200	Strong transcription	GM12878-XiMat	blood
12	chr12:123875600-123884400	Strong transcription	HMEC	breast
13	chr12:123875600-123884600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:123875600-123885400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
17	chr12:123875800-123884200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:123875800-123884600	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:123876000-123884400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:123876200-123884400	Strong transcription	Fetal Lung	lung
22	chr12:123876200-123885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:123876400-123884600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
25	chr12:123876600-123884000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:123876800-123884200	Strong transcription	K562	blood
28	chr12:123876800-123884400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:123876800-123884400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:123876800-123885400	Strong transcription	Fetal Brain Female	brain
31	chr12:123876800-123887600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:123877000-123885000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:123877000-123885600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:123877200-123884400	Strong transcription	Brain Germinal Matrix	brain
35	chr12:123877400-123884400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:123877400-123889000	Weak transcription	Fetal Heart	heart
37	chr12:123877400-123895600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:123877800-123884400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:123878000-123884000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:123878000-123884400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr12:123878200-123884600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:123879000-123884200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:123879000-123884400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr12:123879000-123884600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:123879600-123884600	Strong transcription	Dnd41	blood
46	chr12:123880600-123883800	Genic enhancers	Gastric	stomach
47	chr12:123880600-123884200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:123881000-123884000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:123881000-123884200	Genic enhancers	Brain Substantia Nigra	brain
50	chr12:123881200-123884400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin

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