Variant report

Variant	rs4147666
Chromosome Location	chr12:4757355-4757356
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr12:4757321-4757892	K562	blood:	n/a	n/a
2	POLR2A	chr12:4757126-4758599	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr12:4757259-4758518	MCF10A-Er-Src	breast:	n/a	chr12:4757480-4757491
4	MXI1	chr12:4757107-4759126	SK-N-SH	brain:	n/a	n/a
5	MYC	chr12:4757330-4758468	K562	blood:	n/a	n/a
6	FOS	chr12:4757345-4757771	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr12:4757283-4758486	NB4	blood:	n/a	n/a
8	RELA	chr12:4757276-4758531	GM19099	blood:	n/a	n/a
9	STAT3	chr12:4757227-4758523	MCF10A-Er-Src	breast:	n/a	chr12:4757480-4757491
10	POLR2A	chr12:4757354-4758666	GM12878	blood:	n/a	n/a
11	MTA3	chr12:4757175-4758801	GM12878	blood:	n/a	n/a
12	STAT3	chr12:4757333-4758515	MCF10A-Er-Src	breast:	n/a	chr12:4757480-4757491
13	POLR2A	chr12:4757240-4758656	MCF10A-Er-Src	breast:	n/a	n/a
14	HCFC1	chr12:4757295-4759184	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:4757225-4758826	GM12891	blood:	n/a	n/a
16	MAX	chr12:4757314-4758606	NB4	blood:	n/a	n/a
17	RUNX3	chr12:4757211-4757797	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:4757334-4758749	Raji	blood:	n/a	n/a
19	ESRRA	chr12:4756578-4758766	GM12878	blood:	n/a	chr12:4757367-4757376
20	RUNX3	chr12:4757209-4757637	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:4756960-4758649	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:4757344-4758729	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:4757018..4762059-chr12:4764285..4767290,6	K562	blood:
2	chr12:4756861..4759668-chr12:4760395..4765208,7	MCF-7	breast:
3	chr12:4751073..4755821-chr12:4757118..4761577,5	MCF-7	breast:
4	chr12:4757063..4759938-chr12:4760465..4764038,5	K562	blood:
5	chr12:4754845..4760714-chr12:4761830..4765057,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKAP3-3	chr12:4756240-4758165	NONHSAT025970

Variant related genes	Relation type
AKAP3	TF binding region
NDUFA9	TF binding region
ENSG00000256381	Chromatin interaction
ENSG00000111254	Chromatin interaction
ENSG00000139180	Chromatin interaction
ENSG00000255639	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10744655	0.87[JPT][hapmap]
rs11063280	0.83[EUR][1000 genomes]
rs11063282	0.90[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs11614030	0.88[MEX][hapmap];0.86[TSI][hapmap]
rs12308883	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs12309713	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs12310639	0.94[EUR][1000 genomes]
rs12318966	0.84[EUR][1000 genomes]
rs12811453	0.90[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12829711	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs16931616	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs16931620	0.84[EUR][1000 genomes]
rs1990311	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs2072354	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267548	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2302246	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs35167443	0.86[EUR][1000 genomes]
rs4147667	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147668	0.80[CHB][hapmap];0.83[YRI][hapmap]
rs4147672	0.90[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4147673	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs4147677	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs4147678	0.84[EUR][1000 genomes]
rs4147679	0.80[EUR][1000 genomes]
rs4147680	0.80[EUR][1000 genomes]
rs4147682	0.81[EUR][1000 genomes]
rs4147684	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs4147685	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs4766264	1.00[CEU][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4766267	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7312402	1.00[CEU][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7958182	0.90[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs7972657	0.84[TSI][hapmap]
rs7972920	0.90[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs876586	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4147666	AKAP3	cis	Muscle Skeletal	GTEx
rs4147666	AKAP3	cis	Stomach	GTEx
rs4147666	AKAP3	cis	lung	GTEx
rs4147666	AKAP3	cis	Heart Left Ventricle	GTEx
rs4147666	AKAP3	cis	Esophagus Muscularis	GTEx
rs4147666	AKAP3	cis	Thyroid	GTEx
rs4147666	SCNN1A	cis	cerebellum	SCAN
rs4147666	NDUFA9	cis	parietal	SCAN
rs4147666	AKAP3	cis	cerebellum	SCAN
rs4147666	ADIPOR2	cis	parietal	SCAN
rs4147666	AKAP3	cis	parietal	SCAN
rs4147666	ACRBP	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4737600-4757400	Weak transcription	Pancreas	Pancrea
2	chr12:4755000-4757400	Weak transcription	Aorta	Aorta
3	chr12:4756400-4757600	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr12:4756800-4757400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr12:4756800-4757400	Enhancers	Liver	Liver
6	chr12:4756800-4757400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr12:4756800-4757400	Enhancers	Stomach Mucosa	stomach
8	chr12:4756800-4757400	Enhancers	Thymus	Thymus
9	chr12:4756800-4757800	Flanking Active TSS	GM12878-XiMat	blood
10	chr12:4757000-4757400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:4757000-4757400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:4757000-4757400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:4757000-4757400	Enhancers	Primary B cells from peripheral blood	blood
14	chr12:4757000-4757400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:4757000-4757400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr12:4757000-4757400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:4757000-4757400	Enhancers	Adipose Nuclei	Adipose
18	chr12:4757000-4757400	Enhancers	Brain Cingulate Gyrus	brain
19	chr12:4757000-4757400	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr12:4757000-4757400	Enhancers	Fetal Heart	heart
21	chr12:4757000-4757400	Flanking Active TSS	Fetal Intestine Large	intestine
22	chr12:4757000-4757400	Enhancers	Fetal Lung	lung
23	chr12:4757000-4757400	Enhancers	Fetal Thymus	thymus
24	chr12:4757000-4757400	Enhancers	Spleen	Spleen
25	chr12:4757000-4757400	Flanking Active TSS	HMEC	breast
26	chr12:4757000-4757600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:4757000-4757600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr12:4757000-4757600	Flanking Active TSS	Brain Angular Gyrus	brain
29	chr12:4757000-4757600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr12:4757000-4757600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr12:4757000-4757600	Enhancers	Small Intestine	intestine
32	chr12:4757000-4757600	Flanking Active TSS	NHEK	skin
33	chr12:4757000-4757800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:4757000-4757800	Flanking Active TSS	Dnd41	blood
35	chr12:4757000-4758000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:4757000-4758400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:4757000-4758800	Active TSS	Colonic Mucosa	Colon
38	chr12:4757000-4759200	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr12:4757200-4757400	Enhancers	H1 Cell Line	embryonic stem cell
40	chr12:4757200-4757400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:4757200-4757400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:4757200-4757400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:4757200-4757400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:4757200-4757400	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr12:4757200-4757400	Enhancers	Primary T cells fromperipheralblood	blood
46	chr12:4757200-4757400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr12:4757200-4757400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr12:4757200-4757400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:4757200-4757400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:4757200-4757400	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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