Variant report

Variant	rs7312402
Chromosome Location	chr12:4755517-4755518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:4755479-4755529	A549	lung:	n/a
2	chr12:4755479-4755529	AG09309	skin:	n/a
3	chr12:4755479-4755529	AG10803	skin:	n/a
4	chr12:4755479-4755529	T-47D	breast:	n/a
5	chr12:4755479-4755529	SK-N-SH_RA	brain:	n/a
6	chr12:4755479-4755529	HRCEpiC	kidney:	n/a
7	chr12:4755479-4755529	Jurkat	blood:	n/a
8	chr12:4755479-4755529	HAEpiC	amniotic membrane:	n/a
9	chr12:4755479-4755529	HMEC	breast:	n/a
10	chr12:4755479-4755529	HL-60	blood:	n/a
11	chr12:4755479-4755529	HRPEpiC	eye:	n/a
12	chr12:4755479-4755529	HepG2	liver:	n/a
13	chr12:4755479-4755529	HUVEC	blood vessel:	n/a
14	chr12:4755479-4755529	Hela-S3	cervix:	n/a
15	chr12:4755479-4755529	BE2_C	brain:	n/a
16	chr12:4755479-4755529	PANC-1	pancreas:	n/a
17	chr12:4755479-4755529	PrEC	prostate:	n/a
18	chr12:4755479-4755529	AG04449	skin:	fetal
19	chr12:4755479-4755529	ECC-1	luminal epithelium:	n/a
20	chr12:4755479-4755529	SKMC	muscle:	n/a
21	chr12:4755479-4755529	IMR90	lung:	fetal
22	chr12:4755479-4755529	HEK293	kidney:	embryo
23	chr12:4755479-4755529	GM19239	blood:	n/a
24	chr12:4755479-4755529	HNPCEpiC	eye:	n/a
25	chr12:4755479-4755529	AoSMC	blood vessel:	n/a
26	chr12:4755479-4755529	U87	brain:	n/a
27	chr12:4755479-4755529	AG09319	gingival:	n/a
28	chr12:4755479-4755529	GM12891	blood:	n/a
29	chr12:4755479-4755529	HCT-116	colon:	n/a
30	chr12:4755479-4755529	RPTEC	kidney:	n/a
31	chr12:4755479-4755529	ovcar-3	ovarian:	n/a
32	chr12:4755479-4755529	HCM	heart:	n/a
33	chr12:4755479-4755529	HEEpiC	esophagus:	n/a
34	chr12:4755479-4755529	NHBE	bronchial:	n/a
35	chr12:4755479-4755529	H1-hESC	embryonic stem cell:	embryo
36	chr12:4755479-4755529	ProgFib	skin:	n/a
37	chr12:4755479-4755529	NHDF-neo	bronchial:	n/a
38	chr12:4755479-4755529	K562	blood:	n/a
39	chr12:4755479-4755529	MCF-7	breast:	n/a
40	chr12:4755479-4755529	Caco-2	colon:	n/a
41	chr12:4755479-4755529	GM06990	blood:	n/a
42	chr12:4755479-4755529	PFSK-1	brain:	n/a
43	chr12:4755479-4755529	LNCaP	prostate:	n/a
44	chr12:4755479-4755529	HCF	heart:	n/a
45	chr12:4755479-4755529	GM12892	blood:	n/a
46	chr12:4755479-4755529	NH-A	brain:	n/a
47	chr12:4755479-4755529	SAEC	small airway:	n/a
48	chr12:4755479-4755529	HRE	kidney:	n/a
49	chr12:4755479-4755529	SK-N-SH	brain:	n/a
50	chr12:4755479-4755529	GM12878	blood:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4751073..4755821-chr12:4757118..4761577,5	MCF-7	breast:
2	chr12:4754845..4760714-chr12:4761830..4765057,7	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFA9	CpG island
AKAP3	CpG island
ENSG00000139180	Chromatin interaction
ENSG00000111254	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs11063280	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11063282	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11063285	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs11614030	0.89[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs12303320	0.88[ASN][1000 genomes]
rs12308883	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12309713	0.90[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12310639	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12313377	0.88[ASN][1000 genomes]
rs12318966	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12811453	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]
rs12828416	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs12829711	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16931616	0.89[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16931620	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1860343	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs1990311	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2072354	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2267548	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299833	0.87[ASN][1000 genomes]
rs2302246	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884671	0.81[ASN][1000 genomes]
rs35131771	0.86[ASN][1000 genomes]
rs35167443	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147666	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]
rs4147667	0.90[CEU][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4147671	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs4147672	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147673	0.89[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147677	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147678	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147679	0.95[ASN][1000 genomes]
rs4147680	0.95[ASN][1000 genomes]
rs4147682	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4147684	0.89[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147685	0.93[CHB][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs4766264	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4766267	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4766269	0.93[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs61909965	0.95[ASN][1000 genomes]
rs7136668	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7958182	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972657	0.93[CHB][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.95[ASN][1000 genomes]
rs7972737	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7972920	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7975484	0.86[ASN][1000 genomes]
rs7977981	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs876586	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7312402	AKAP3	cis	Esophagus Muscularis	GTEx
rs7312402	ACRBP	cis	parietal	SCAN
rs7312402	AKAP3	cis	lung	GTEx
rs7312402	ADIPOR2	cis	parietal	SCAN
rs7312402	AKAP3	cis	Muscle Skeletal	GTEx
rs7312402	AKAP3	cis	Thyroid	GTEx
rs7312402	NDUFA9	cis	parietal	SCAN
rs7312402	AKAP3	cis	cerebellum	SCAN
rs7312402	SCNN1A	cis	cerebellum	SCAN
rs7312402	AKAP3	cis	Heart Left Ventricle	GTEx
rs7312402	AKAP3	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4724200-4756800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr12:4737600-4757400	Weak transcription	Pancreas	Pancrea
3	chr12:4737800-4757200	Weak transcription	Brain Anterior Caudate	brain
4	chr12:4745400-4757200	Weak transcription	Brain Substantia Nigra	brain
5	chr12:4746600-4757000	Weak transcription	Small Intestine	intestine
6	chr12:4754000-4756600	Weak transcription	GM12878-XiMat	blood
7	chr12:4754400-4757200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:4754600-4756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:4754800-4757200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:4755000-4757000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:4755000-4757400	Weak transcription	Aorta	Aorta

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