Variant report

Variant	rs4147668
Chromosome Location	chr12:4757809-4757810
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:151)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:151 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr12:4757537-4758703	H1-hESC	embryonic stem cell:	n/a	n/a
2	RUNX3	chr12:4757725-4758567	GM12878	blood:	n/a	n/a
3	TEAD4	chr12:4757321-4757892	K562	blood:	n/a	n/a
4	POLR2A	chr12:4757126-4758599	MCF10A-Er-Src	breast:	n/a	n/a
5	TBL1XR1	chr12:4757426-4758524	GM12878	blood:	n/a	n/a
6	STAT3	chr12:4757259-4758518	MCF10A-Er-Src	breast:	n/a	chr12:4757480-4757491
7	YY1	chr12:4757781-4758894	SK-N-SH	brain:	n/a	chr12:4758282-4758302 chr12:4757987-4758004 chr12:4758288-4758300
8	POLR2A	chr12:4757581-4758605	GM19193	blood:	n/a	n/a
9	POLR2A	chr12:4757758-4758652	PFSK-1	brain:	n/a	n/a
10	MXI1	chr12:4757107-4759126	SK-N-SH	brain:	n/a	n/a
11	REST	chr12:4757476-4759419	H1-neurons	neurons:	n/a	n/a
12	MAX	chr12:4757530-4758433	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:4757603-4758640	Hela-S3	cervix:	n/a	n/a
14	SP1	chr12:4757786-4758644	A549	lung:	n/a	n/a
15	POLR2A	chr12:4757657-4758587	K562	blood:	n/a	n/a
16	TCF12	chr12:4757783-4758724	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr12:4757367-4758571	GM12878	blood:	n/a	n/a
18	SIN3A	chr12:4757582-4758974	H1-hESC	embryonic stem cell:	n/a	chr12:4758562-4758570
19	POLR2A	chr12:4757556-4758695	H1-neurons	neurons:	n/a	n/a
20	MAX	chr12:4757462-4758635	A549	lung:	n/a	n/a
21	REST	chr12:4757652-4758799	A549	lung:	n/a	n/a
22	POLR2A	chr12:4757502-4758642	Hela-S3	cervix:	n/a	n/a
23	YY1	chr12:4757730-4758668	H1-hESC	embryonic stem cell:	n/a	chr12:4758282-4758302 chr12:4757987-4758004 chr12:4758288-4758300
24	TCF12	chr12:4757797-4758694	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr12:4757598-4758545	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:4757628-4758685	K562	blood:	n/a	n/a
27	MAZ	chr12:4757755-4758617	Hela-S3	cervix:	n/a	n/a
28	MYC	chr12:4757330-4758468	K562	blood:	n/a	n/a
29	POLR2A	chr12:4757725-4758493	HEK293	kidney:	n/a	n/a
30	POLR2A	chr12:4757655-4758910	K562	blood:	n/a	n/a
31	MAX	chr12:4757429-4758616	Hela-S3	cervix:	n/a	n/a
32	TAF1	chr12:4757695-4758833	ECC-1	luminal epithelium:	n/a	n/a
33	ZNF263	chr12:4757762-4758643	HEK293-T-REx	kidney:	n/a	n/a
34	MAX	chr12:4757589-4758545	K562	blood:	n/a	n/a
35	POLR2A	chr12:4757674-4758864	K562	blood:	n/a	n/a
36	POLR2A	chr12:4757562-4758670	GM12892	blood:	n/a	n/a
37	TBP	chr12:4757649-4758544	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr12:4757610-4758537	K562	blood:	n/a	n/a
39	RFX5	chr12:4757673-4758883	Hela-S3	cervix:	n/a	n/a
40	GTF2B	chr12:4757775-4758379	K562	blood:	n/a	n/a
41	RCOR1	chr12:4757658-4758451	K562	blood:	n/a	n/a
42	ARID3A	chr12:4757430-4758315	K562	blood:	n/a	n/a
43	MYC	chr12:4757283-4758486	NB4	blood:	n/a	n/a
44	USF2	chr12:4757753-4758416	Hela-S3	cervix:	n/a	n/a
45	BHLHE40	chr12:4757761-4758471	K562	blood:	n/a	n/a
46	KAP1	chr12:4757565-4758872	HEK293	kidney:	n/a	chr12:4757802-4757810 chr12:4758453-4758461
47	TBP	chr12:4757585-4758624	H1-hESC	embryonic stem cell:	n/a	n/a
48	JUND	chr12:4757473-4758631	K562	blood:	n/a	chr12:4758116-4758125 chr12:4757905-4757913
49	MXI1	chr12:4757742-4758477	H1-hESC	embryonic stem cell:	n/a	n/a
50	SMC3	chr12:4757720-4758572	Hela-S3	cervix:	n/a	chr12:4758361-4758371

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:4757759-4757809	T-47D	breast:	n/a
2	chr12:4757759-4757809	SK-N-SH_RA	brain:	n/a
3	chr12:4757759-4757809	NH-A	brain:	n/a
4	chr12:4757759-4757809	BJ	skin:	n/a
5	chr12:4757759-4757809	SK-N-MC	brain:	n/a
6	chr12:4757759-4757809	SKMC	muscle:	n/a
7	chr12:4757759-4757809	HRE	kidney:	n/a
8	chr12:4757759-4757809	HEK293	kidney:	embryo
9	chr12:4757759-4757809	HUVEC	blood vessel:	n/a
10	chr12:4757759-4757809	HCPEpiC	choroid plexus:	n/a
11	chr12:4757759-4757809	BE2_C	brain:	n/a
12	chr12:4757759-4757809	HEEpiC	esophagus:	n/a
13	chr12:4757759-4757809	AG09309	skin:	n/a
14	chr12:4757759-4757809	GM12891	blood:	n/a
15	chr12:4757759-4757809	HRCEpiC	kidney:	n/a
16	chr12:4757759-4757809	NB4	blood:	n/a
17	chr12:4757759-4757809	PFSK-1	brain:	n/a
18	chr12:4757759-4757809	GM12878	blood:	n/a
19	chr12:4757759-4757809	HCM	heart:	n/a
20	chr12:4757759-4757809	CMK	blood:	n/a
21	chr12:4757759-4757809	PrEC	prostate:	n/a
22	chr12:4757759-4757809	U87	brain:	n/a
23	chr12:4757759-4757809	Jurkat	blood:	n/a
24	chr12:4757759-4757809	K562	blood:	n/a
25	chr12:4757759-4757809	HMEC	breast:	n/a
26	chr12:4757759-4757809	HCT-116	colon:	n/a
27	chr12:4757759-4757809	HL-60	blood:	n/a
28	chr12:4757759-4757809	AoSMC	blood vessel:	n/a
29	chr12:4757759-4757809	HNPCEpiC	eye:	n/a
30	chr12:4757759-4757809	HCF	heart:	n/a
31	chr12:4757759-4757809	MCF10A-Er-Src	breast:	n/a
32	chr12:4757759-4757809	SK-N-SH	brain:	n/a
33	chr12:4757759-4757809	AG10803	skin:	n/a
34	chr12:4757759-4757809	ProgFib	skin:	n/a
35	chr12:4757759-4757809	AG04450	lung:	fetal
36	chr12:4757759-4757809	SAEC	small airway:	n/a
37	chr12:4757759-4757809	HIPEpiC	eye:	n/a
38	chr12:4757759-4757809	AG04449	skin:	fetal
39	chr12:4757759-4757809	NHBE	bronchial:	n/a
40	chr12:4757759-4757809	HRPEpiC	eye:	n/a
41	chr12:4757759-4757809	HepG2	liver:	n/a
42	chr12:4757759-4757809	GM06990	blood:	n/a
43	chr12:4757759-4757809	Caco-2	colon:	n/a
44	chr12:4757759-4757809	HPAEpiC	pulmonary alveolar:	n/a
45	chr12:4757759-4757809	ovcar-3	ovarian:	n/a
46	chr12:4757759-4757809	NT2-D1	testis:	n/a
47	chr12:4757759-4757809	MCF-7	breast:	n/a
48	chr12:4757759-4757809	PANC-1	pancreas:	n/a
49	chr12:4757759-4757809	GM12892	blood:	n/a
50	chr12:4757759-4757809	AG09319	gingival:	n/a

(count:7 , 50 per page) page: 1

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	chr12:4757537..4758351-chr2:9983167..9983703,2	Hela-S3	cervix:
6	chr12:4754845..4760714-chr12:4761830..4765057,7	MCF-7	breast:
7	chr12:4757573..4759938-chr12:4760465..4764276,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKAP3-3	chr12:4756240-4758165	NONHSAT025970
2	lnc-AKAP3-3	chr12:4757620-4758174	NONHSAT025968

No data

Variant related genes	Relation type
NDUFA9	TF binding region
AKAP3	TF binding region
NDUFA9	CpG island
AKAP3	CpG island
ENSG00000255639	Chromatin interaction
ENSG00000256381	Chromatin interaction
ENSG00000115750	Chromatin interaction
ENSG00000111254	Chromatin interaction
ENSG00000139180	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10774255	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11609763	0.88[ASN][1000 genomes]
rs11610695	0.88[ASN][1000 genomes]
rs11615279	0.88[ASN][1000 genomes]
rs1990314	0.88[ASN][1000 genomes]
rs2270134	0.84[EUR][1000 genomes]
rs3753147	0.88[ASN][1000 genomes]
rs4147666	0.80[CHB][hapmap];0.83[YRI][hapmap]
rs4147667	0.80[CHB][hapmap];0.83[YRI][hapmap]
rs7134765	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs714621	0.81[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4147668	AKAP3	Cis_1M	lymphoblastoid	RTeQTL
rs4147668	AKAP3	cis	Stomach	GTEx
rs4147668	AKAP3	cis	Esophagus Mucosa	GTEx
rs4147668	AKAP3	cis	Esophagus Muscularis	GTEx
rs4147668	AKAP3	cis	Thyroid	GTEx
rs4147668	AKAP3	cis	Muscle Skeletal	GTEx
rs4147668	AKAP3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4757000-4758000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:4757000-4758400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:4757000-4758800	Active TSS	Colonic Mucosa	Colon
4	chr12:4757000-4759200	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr12:4757200-4758000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr12:4757200-4758000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr12:4757200-4758200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:4757200-4758800	Active TSS	Brain Hippocampus Middle	brain
9	chr12:4757200-4758800	Active TSS	Fetal Stomach	stomach
10	chr12:4757200-4758800	Active TSS	Stomach Smooth Muscle	stomach
11	chr12:4757200-4759000	Active TSS	NHLF	lung
12	chr12:4757200-4759200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:4757200-4759200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:4757200-4759200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:4757200-4759400	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr12:4757200-4759400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:4757200-4759400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:4757200-4759400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:4757200-4759400	Active TSS	K562	blood
20	chr12:4757200-4759400	Active TSS	NHDF-Ad	bronchial
21	chr12:4757200-4760200	Active TSS	Right Atrium	heart
22	chr12:4757400-4758000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr12:4757400-4758000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr12:4757400-4758000	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr12:4757400-4758800	Active TSS	Brain Cingulate Gyrus	brain
26	chr12:4757400-4758800	Active TSS	Brain Germinal Matrix	brain
27	chr12:4757400-4758800	Active TSS	Duodenum Mucosa	Duodenum
28	chr12:4757400-4758800	Active TSS	Fetal Brain Male	brain
29	chr12:4757400-4758800	Active TSS	Placenta	Placenta
30	chr12:4757400-4759000	Active TSS	Aorta	Aorta
31	chr12:4757400-4759000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr12:4757400-4759000	Active TSS	Fetal Lung	lung
33	chr12:4757400-4759000	Active TSS	Pancreas	Pancrea
34	chr12:4757400-4759000	Active TSS	Osteobl	bone
35	chr12:4757400-4759200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:4757400-4759200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:4757400-4759200	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr12:4757400-4759200	Active TSS	Muscle Satellite Cultured Cells	--
39	chr12:4757400-4759200	Active TSS	Fetal Intestine Large	intestine
40	chr12:4757400-4759200	Active TSS	Fetal Muscle Trunk	muscle
41	chr12:4757400-4759200	Active TSS	Ovary	ovary
42	chr12:4757400-4759200	Active TSS	A549	lung
43	chr12:4757400-4759200	Active TSS	HSMMtube	muscle
44	chr12:4757400-4759400	Active TSS	Fetal Intestine Small	intestine
45	chr12:4757400-4759600	Active TSS	H1 Cell Line	embryonic stem cell
46	chr12:4757400-4759600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:4757400-4759800	Active TSS	Psoas Muscle	Psoas
48	chr12:4757400-4759800	Active TSS	Right Ventricle	heart
49	chr12:4757600-4758000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:4757600-4758600	Active TSS	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links