Variant report

Variant	rs28410096
Chromosome Location	chr12:123880862-123880863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123879282..123881067-chr12:123885695..123887495,2	MCF-7	breast:
2	chr12:123879767..123882314-chr12:123882742..123884960,2	MCF-7	breast:
3	chr12:123873357..123876856-chr12:123879238..123882589,5	K562	blood:
4	chr12:123866827..123868502-chr12:123879213..123881097,2	K562	blood:

Variant related genes	Relation type
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 177 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:173)

rs_ID	r²[population]
rs10082867	0.84[AMR][1000 genomes];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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs10773006	0.97[ASN][1000 genomes]
rs10773007	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs10773014	1.00[YRI][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];1.00[YRI][hapmap]
rs10846510	1.00[YRI][hapmap]
rs10846514	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs10846517	0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10846518	0.82[GIH][hapmap];1.00[YRI][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];1.00[YRI][hapmap]
rs11057238	0.85[ASN][1000 genomes]
rs11057240	1.00[YRI][hapmap]
rs11057242	0.93[ASN][1000 genomes]
rs11057248	0.93[ASN][1000 genomes]
rs11057250	1.00[YRI][hapmap]
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];1.00[YRI][hapmap]
rs11057273	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];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	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];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	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11611677	0.96[ASN][1000 genomes]
rs11611679	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11611680	0.94[ASN][1000 genomes]
rs11611694	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11612234	0.81[ASN][1000 genomes]
rs12317103	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12317452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12366872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12367421	0.95[ASN][1000 genomes]
rs12371973	1.00[YRI][hapmap]
rs12582153	0.95[ASN][1000 genomes]
rs13303208	0.94[ASN][1000 genomes]
rs1402275	0.85[YRI][hapmap]
rs1568428	0.94[JPT][hapmap]
rs1790104	0.85[JPT][hapmap]
rs1879379	0.94[JPT][hapmap]
rs2271976	1.00[CEU][hapmap];0.94[JPT][hapmap]
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	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28475177	0.82[GIH][hapmap];1.00[YRI][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	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28516750	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28517382	0.81[ASN][1000 genomes]
rs28532037	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]
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	1.00[AFR][1000 genomes];1.00[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	1.00[AFR][1000 genomes];1.00[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];1.00[YRI][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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28820735	0.95[AFR][1000 genomes];1.00[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	0.93[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];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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	1.00[YRI][hapmap];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];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];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[AFR][1000 genomes];0.81[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	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];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];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];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[AMR][1000 genomes];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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];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	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9669295	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9705407	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9739171	0.98[AFR][1000 genomes];0.86[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: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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28410096	CDK2AP1	cis	Whole Blood	GTEx
rs28410096	RP11-282O18.3	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875000-123881000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:123875000-123884400	Strong transcription	Thymus	Thymus
3	chr12:123875000-123886400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:123875200-123881000	Strong transcription	Fetal Intestine Large	intestine
5	chr12:123875200-123884400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:123875200-123884600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:123875200-123894400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:123875400-123882200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:123875400-123882600	Strong transcription	Placenta	Placenta
10	chr12:123875400-123883600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:123875400-123884600	Strong transcription	Primary T cells from cord blood	blood
12	chr12:123875600-123881000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:123875600-123881600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:123875600-123882200	Strong transcription	Colon Smooth Muscle	Colon
15	chr12:123875600-123882800	Weak transcription	Psoas Muscle	Psoas
16	chr12:123875600-123884000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:123875600-123884200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:123875600-123884200	Strong transcription	A549	lung
19	chr12:123875600-123884200	Strong transcription	GM12878-XiMat	blood
20	chr12:123875600-123884400	Strong transcription	HMEC	breast
21	chr12:123875600-123884600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:123875600-123885400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
25	chr12:123875800-123881200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr12:123875800-123881800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:123875800-123881800	Strong transcription	NH-A	brain
28	chr12:123875800-123882000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:123875800-123882200	Strong transcription	NHEK	skin
30	chr12:123875800-123884200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:123875800-123884600	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:123876000-123884400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:123876200-123882800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:123876200-123884400	Strong transcription	Fetal Lung	lung
36	chr12:123876200-123885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:123876400-123881400	Strong transcription	Fetal Stomach	stomach
38	chr12:123876400-123882600	Strong transcription	Liver	Liver
39	chr12:123876400-123884600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
41	chr12:123876600-123881600	Strong transcription	HSMM	muscle
42	chr12:123876600-123881800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr12:123876600-123881800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr12:123876600-123882000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:123876600-123882000	Strong transcription	HSMMtube	muscle
46	chr12:123876600-123884000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:123876800-123881400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:123876800-123882200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:123876800-123882400	Strong transcription	Hela-S3	cervix

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