Variant report

Variant	rs12811453
Chromosome Location	chr12:4761011-4761012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:4757018..4762059-chr12:4764285..4767290,6	K562	blood:
2	chr12:4757063..4759938-chr12:4760465..4764038,5	K562	blood:
3	chr12:4756861..4759668-chr12:4760395..4765208,7	MCF-7	breast:
4	chr12:4757573..4759938-chr12:4760465..4764276,3	K562	blood:
5	chr12:4751073..4755821-chr12:4757118..4761577,5	MCF-7	breast:
6	chr12:4757989..4759732-chr12:4759874..4761785,2	MCF-7	breast:
7	chr12:4758381..4761405-chr12:4778974..4782071,3	K562	blood:

Variant related genes	Relation type
ENSG00000255639	Chromatin interaction
ENSG00000139180	Chromatin interaction
ENSG00000256381	Chromatin interaction
ENSG00000111254	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11063280	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063285	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11614014	0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11614030	1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12303320	0.85[ASN][1000 genomes]
rs12308883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309713	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12310639	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12313377	0.87[ASN][1000 genomes]
rs12318966	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12828416	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs12829711	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs16931616	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16931620	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860343	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs1990311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072354	0.82[EUR][1000 genomes]
rs2267548	0.90[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299833	0.86[ASN][1000 genomes]
rs2302246	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35131771	0.82[ASN][1000 genomes]
rs35167443	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147666	0.90[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs4147667	0.88[MEX][hapmap];0.84[TSI][hapmap]
rs4147671	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147673	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147677	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147678	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147679	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147680	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147682	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147684	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147685	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766264	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4766267	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4766269	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61909965	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136668	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs7312402	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958182	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972657	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972737	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs7972920	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975484	0.82[ASN][1000 genomes]
rs7977981	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs876586	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv898617	chr12:4715082-4768619	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898618	chr12:4726068-4764137	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv898619	chr12:4737715-4771456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv898620	chr12:4745313-4771456	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv557125	chr12:4748410-4764137	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1036308	chr12:4748657-4804156	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv898621	chr12:4751798-4768193	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv898622	chr12:4751798-4768619	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv898623	chr12:4751798-4771456	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv898624	chr12:4757474-4769876	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv557126	chr12:4757809-4768619	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv898625	chr12:4759380-4771682	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12811453	AKAP3	cis	Thyroid	GTEx
rs12811453	NDUFA9	cis	parietal	SCAN
rs12811453	AKAP3	cis	parietal	SCAN
rs12811453	ADIPOR2	cis	parietal	SCAN
rs12811453	SCNN1A	cis	cerebellum	SCAN
rs12811453	ACRBP	cis	parietal	SCAN
rs12811453	AKAP3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4758800-4763400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:4759000-4763000	Weak transcription	Placenta	Placenta
3	chr12:4759000-4763400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:4759000-4763400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:4759000-4763400	Weak transcription	Spleen	Spleen
6	chr12:4759000-4764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:4759000-4764000	Weak transcription	Lung	lung
8	chr12:4759000-4764200	Weak transcription	Esophagus	oesophagus
9	chr12:4759000-4764400	Weak transcription	Aorta	Aorta
10	chr12:4759000-4764400	Weak transcription	Pancreas	Pancrea
11	chr12:4759000-4772600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:4759000-4799400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:4759200-4763400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:4759200-4763400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:4759200-4763400	Weak transcription	Ovary	ovary
16	chr12:4759200-4763400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:4759200-4764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:4759200-4764400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:4759200-4776200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:4759400-4761200	Enhancers	Colon Smooth Muscle	Colon
21	chr12:4759400-4761400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:4759400-4762200	Enhancers	Liver	Liver
23	chr12:4759400-4762600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr12:4759400-4763400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr12:4759400-4763400	Weak transcription	HSMMtube	muscle
26	chr12:4759400-4764800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:4759400-4767200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:4759600-4761400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr12:4759600-4761800	Enhancers	HepG2	liver
30	chr12:4759600-4763000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:4759600-4763400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:4759600-4763400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:4759600-4763400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:4759600-4763400	Weak transcription	Left Ventricle	heart
35	chr12:4759600-4763400	Weak transcription	NH-A	brain
36	chr12:4759600-4764400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:4759600-4764800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:4759600-4767000	Weak transcription	Stomach Mucosa	stomach
39	chr12:4759800-4761200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:4759800-4761800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:4759800-4763200	Weak transcription	HSMM	muscle
42	chr12:4759800-4763400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:4759800-4763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr12:4759800-4763400	Weak transcription	Fetal Kidney	kidney
45	chr12:4759800-4763400	Weak transcription	Fetal Stomach	stomach
46	chr12:4759800-4763400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:4759800-4763600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:4759800-4763600	Weak transcription	Colonic Mucosa	Colon
49	chr12:4759800-4764200	Weak transcription	NHLF	lung
50	chr12:4760000-4761200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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