Variant report

Variant	rs28636834
Chromosome Location	chr12:123871070-123871071
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123717467..123721119-chr12:123869942..123873013,3	K562	blood:
2	chr12:123845591..123852236-chr12:123866929..123875043,19	MCF-7	breast:
3	chr12:123715746..123718967-chr12:123870796..123875270,4	K562	blood:
4	chr12:123755164..123758333-chr12:123868507..123873426,5	K562	blood:
5	chr12:123458609..123460830-chr12:123870435..123872750,2	K562	blood:
6	chr12:123868443..123871332-chr12:123941328..123944744,4	K562	blood:
7	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
8	chr12:123839967..123842142-chr12:123869502..123871967,2	MCF-7	breast:
9	chr12:123868884..123871155-chr12:123942728..123944363,2	MCF-7	breast:
10	chr12:123870684..123873491-chr12:123941342..123943069,2	MCF-7	breast:
11	chr12:123754759..123757395-chr12:123866766..123872450,7	MCF-7	breast:
12	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
13	chr12:123870366..123875219-chr12:124064500..124069174,6	K562	blood:
14	chr12:123869164..123871955-chr12:123947898..123950371,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000086598	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000256028	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1060105	0.89[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs10772998	0.83[CEU][hapmap]
rs10773002	0.81[GIH][hapmap]
rs10846486	0.89[CEU][hapmap]
rs11057192	0.83[CEU][hapmap];0.97[TSI][hapmap]
rs11057270	0.81[EUR][1000 genomes]
rs11830103	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs12298826	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs12299125	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12304248	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12316131	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes]
rs12322888	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs12817892	0.91[CEU][hapmap]
rs1402274	0.89[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1402275	0.93[GIH][hapmap]
rs1533703	0.81[CEU][hapmap]
rs1568427	0.85[GIH][hapmap]
rs1609520	0.85[GIH][hapmap]
rs1716160	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1716170	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1716171	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1727320	0.89[CEU][hapmap]
rs1727323	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1727324	0.89[CEU][hapmap]
rs1727325	0.89[CEU][hapmap]
rs1727331	0.85[GIH][hapmap]
rs1790095	0.89[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1790131	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1879380	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1969354	0.84[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1980252	0.84[CEU][hapmap]
rs2337934	0.84[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap]
rs2682434	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs2695478	0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs28372579	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28406193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28413626	0.94[EUR][1000 genomes]
rs28458312	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28472704	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28481863	0.81[EUR][1000 genomes]
rs28569885	0.83[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs28576953	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28582096	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28583837	0.99[EUR][1000 genomes]
rs28592876	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28625019	0.89[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs28675824	0.94[EUR][1000 genomes]
rs28676499	0.82[EUR][1000 genomes]
rs28683528	0.92[EUR][1000 genomes]
rs28706696	0.89[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs28715490	0.82[EUR][1000 genomes]
rs28809230	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28855757	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34997336	0.83[EUR][1000 genomes]
rs4372492	0.89[CEU][hapmap]
rs4460848	0.84[TSI][hapmap]
rs4759371	0.84[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4759409	0.84[CEU][hapmap]
rs4759415	0.84[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4930718	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs4930719	0.82[EUR][1000 genomes]
rs6488868	0.88[ASW][hapmap]
rs6576	0.80[AMR][1000 genomes]
rs67624109	0.84[EUR][1000 genomes]
rs7304782	0.85[GIH][hapmap]
rs7313483	0.83[CEU][hapmap]
rs7485502	0.91[EUR][1000 genomes]
rs7953929	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs7955457	0.81[EUR][1000 genomes]
rs7980687	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs941305	0.89[CEU][hapmap]
rs941306	0.89[CEU][hapmap]

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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28636834	CDK2AP1	cis	lymphoblastoid	seeQTL
rs28636834	RP11-282O18.3	cis	Adipose Subcutaneous	GTEx
rs28636834	CDK2AP1	cis	Adipose Subcutaneous	GTEx
rs28636834	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28636834	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28636834	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28636834	PITPNM2	cis	cerebellum	SCAN
rs28636834	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28636834	ANAPC5	cis	parietal	SCAN
rs28636834	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28636834	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28636834	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123869400-123872000	Weak transcription	Stomach Mucosa	stomach
2	chr12:123869600-123871400	Weak transcription	Psoas Muscle	Psoas
3	chr12:123869600-123871800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:123869600-123871800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr12:123869600-123871800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:123869600-123871800	Weak transcription	Esophagus	oesophagus
7	chr12:123869600-123871800	Weak transcription	Fetal Heart	heart
8	chr12:123869600-123871800	Weak transcription	Left Ventricle	heart
9	chr12:123869600-123871800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:123869600-123871800	Weak transcription	Spleen	Spleen
11	chr12:123869600-123872000	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:123869600-123872000	Weak transcription	Pancreas	Pancrea
13	chr12:123869600-123872000	Weak transcription	HSMM	muscle
14	chr12:123869600-123872200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:123869600-123872200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:123869600-123872200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:123869600-123872200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:123869600-123872200	Weak transcription	Adipose Nuclei	Adipose
19	chr12:123869600-123872200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:123869600-123872200	Weak transcription	Fetal Brain Male	brain
21	chr12:123869600-123872200	Weak transcription	Placenta	Placenta
22	chr12:123869600-123872200	Weak transcription	Gastric	stomach
23	chr12:123869600-123872200	Weak transcription	Lung	lung
24	chr12:123869600-123872200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:123869600-123872200	Weak transcription	Right Atrium	heart
26	chr12:123869600-123872200	Weak transcription	Right Ventricle	heart
27	chr12:123869600-123872200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:123869600-123872200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:123869600-123872200	Weak transcription	HSMMtube	muscle
30	chr12:123869600-123872400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:123869600-123872400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:123869600-123872400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:123869600-123872400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:123869600-123872400	Weak transcription	Brain Angular Gyrus	brain
35	chr12:123869600-123872400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:123869600-123872400	Weak transcription	Brain Germinal Matrix	brain
37	chr12:123869600-123872400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:123869600-123872400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:123869600-123872400	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:123869600-123872400	Enhancers	Fetal Intestine Small	intestine
41	chr12:123869600-123872600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:123869600-123872600	Weak transcription	Ovary	ovary
43	chr12:123869600-123872600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:123869600-123872600	Weak transcription	Small Intestine	intestine
45	chr12:123869600-123873000	Weak transcription	Aorta	Aorta
46	chr12:123869800-123871400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:123869800-123871800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr12:123869800-123871800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:123869800-123871800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:123869800-123871800	Weak transcription	Fetal Muscle Leg	muscle

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