Variant report

Variant	rs12809335
Chromosome Location	chr12:30848675-30848676
allele	C/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	MAX	chr12:30847888-30849229	K562	blood:	n/a	chr12:30849010-30849020 chr12:30848696-30848706
2	UBTF	chr12:30848202-30849135	K562	blood:	n/a	n/a
3	ZBTB7A	chr12:30847745-30849139	ECC-1	luminal epithelium:	n/a	chr12:30848668-30848677 chr12:30848746-30848755 chr12:30848455-30848462
4	MAX	chr12:30848598-30849207	SK-N-SH	brain:	n/a	chr12:30849010-30849020 chr12:30848696-30848706
5	REST	chr12:30848568-30849292	A549	lung:	n/a	n/a
6	JUND	chr12:30848649-30848833	H1-hESC	embryonic stem cell:	n/a	chr12:30848814-30848823
7	ZBTB7A	chr12:30847902-30849038	ECC-1	luminal epithelium:	n/a	chr12:30848668-30848677 chr12:30848746-30848755 chr12:30848455-30848462
8	EP300	chr12:30848609-30849007	H1-hESC	embryonic stem cell:	n/a	chr12:30848900-30848909 chr12:30848826-30848840
9	TCF12	chr12:30848536-30849015	GM12878	blood:	n/a	n/a
10	CTCF	chr12:30847780-30849063	K562	blood:	n/a	chr12:30848584-30848593 chr12:30848712-30848725 chr12:30848442-30848455
11	TBL1XR1	chr12:30848093-30849200	K562	blood:	n/a	n/a
12	ZNF143	chr12:30848428-30849197	GM12878	blood:	n/a	chr12:30848693-30848703
13	POLR2A	chr12:30848511-30849252	GM12892	blood:	n/a	n/a
14	ELF1	chr12:30848141-30849169	GM12878	blood:	n/a	chr12:30848599-30848611 chr12:30848831-30848842
15	ETS1	chr12:30848621-30849166	K562	blood:	n/a	n/a
16	FOXM1	chr12:30848620-30849075	GM12878	blood:	n/a	n/a
17	RCOR1	chr12:30847290-30849259	K562	blood:	n/a	n/a
18	HEY1	chr12:30848382-30849226	HepG2	liver:	n/a	chr12:30848596-30848611
19	POLR2A	chr12:30848507-30849247	PANC-1	pancreas:	n/a	n/a
20	CTCF	chr12:30848652-30848798	GM19238	blood:	n/a	chr12:30848712-30848725
21	POLR2A	chr12:30848579-30849090	HUVEC	blood vessel:	n/a	n/a
22	ZNF143	chr12:30848399-30849262	Hela-S3	cervix:	n/a	chr12:30848693-30848703 chr12:30848418-30848436
23	POLR2A	chr12:30848301-30849145	ECC-1	luminal epithelium:	n/a	n/a
24	ZMIZ1	chr12:30848239-30849190	K562	blood:	n/a	n/a
25	RUNX3	chr12:30848513-30849082	GM12878	blood:	n/a	n/a
26	ATF3	chr12:30848656-30848999	HepG2	liver:	n/a	n/a
27	JUND	chr12:30848016-30849098	H1-hESC	embryonic stem cell:	n/a	chr12:30848814-30848823
28	ZNF263	chr12:30847581-30849241	HEK293-T-REx	kidney:	n/a	chr12:30848821-30848842
29	CHD2	chr12:30848522-30849185	K562	blood:	n/a	chr12:30848743-30848753
30	POLR2A	chr12:30848617-30849073	A549	lung:	n/a	n/a
31	POLR2A	chr12:30848609-30849484	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr12:30848423-30848842	HepG2	liver:	n/a	n/a
33	POLR2A	chr12:30847870-30849248	ECC-1	luminal epithelium:	n/a	n/a
34	TAF1	chr12:30848619-30849071	SK-N-SH	brain:	n/a	n/a
35	CTCF	chr12:30848657-30848756	GM19240	blood:	n/a	chr12:30848712-30848725
36	EGR1	chr12:30848425-30849172	HCT-116	colon:	n/a	chr12:30848599-30848609 chr12:30848697-30848707 chr12:30848767-30848777
37	CHD2	chr12:30847925-30849170	Hela-S3	cervix:	n/a	chr12:30848743-30848753
38	POLR2A	chr12:30848551-30849126	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr12:30848525-30849229	GM12892	blood:	n/a	n/a
40	YY1	chr12:30848261-30849243	NT2-D1	testis:	n/a	chr12:30848444-30848458 chr12:30848347-30848358 chr12:30848597-30848608 chr12:30848905-30848927
41	YY1	chr12:30848171-30849233	HepG2	liver:	n/a	chr12:30848444-30848458 chr12:30848347-30848358 chr12:30848597-30848608 chr12:30848905-30848927
42	POLR2A	chr12:30848365-30848872	H1-hESC	embryonic stem cell:	n/a	n/a
43	CEBPD	chr12:30848584-30848914	HepG2	liver:	n/a	n/a
44	JUND	chr12:30847906-30849367	K562	blood:	n/a	chr12:30848814-30848823
45	REST	chr12:30847845-30849472	H1-neurons	neurons:	n/a	chr12:30848432-30848445 chr12:30848419-30848432
46	POLR2A	chr12:30848396-30849304	GM12892	blood:	n/a	n/a
47	POLR2A	chr12:30848582-30849557	K562	blood:	n/a	n/a
48	MXI1	chr12:30848551-30849362	GM12878	blood:	n/a	n/a
49	MAX	chr12:30848498-30849117	HepG2	liver:	n/a	chr12:30849010-30849020 chr12:30848696-30848706
50	POLR2A	chr12:30848137-30849424	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30840558..30845484-chr12:30846630..30850252,8	K562	blood:
2	chr12:30848203..30850367-chr12:31477649..31479869,2	K562	blood:

Variant related genes	Relation type
IPO8	TF binding region
ENSG00000139146	Chromatin interaction
ENSG00000133704	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10444423	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734793	0.85[ASN][1000 genomes]
rs10743729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771745	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771756	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771757	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771760	0.86[ASN][1000 genomes]
rs10771761	0.86[ASN][1000 genomes]
rs10771762	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771768	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs10843804	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843813	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843814	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843815	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843818	0.86[ASN][1000 genomes]
rs10843819	0.86[ASN][1000 genomes]
rs10843820	0.86[ASN][1000 genomes]
rs10843821	0.86[ASN][1000 genomes]
rs10843822	0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843823	0.86[ASN][1000 genomes]
rs10843824	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843827	0.85[ASN][1000 genomes]
rs10843828	0.85[ASN][1000 genomes]
rs10843829	0.83[ASN][1000 genomes]
rs10843831	0.84[ASN][1000 genomes]
rs10843832	0.85[ASN][1000 genomes]
rs10843833	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10843834	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843835	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs11051005	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051008	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051010	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11051027	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051045	0.86[ASN][1000 genomes]
rs11051047	0.85[ASN][1000 genomes]
rs11051048	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051049	0.85[ASN][1000 genomes]
rs11051050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051053	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs11051061	0.84[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11051063	0.81[ASN][1000 genomes]
rs11835180	0.85[ASN][1000 genomes]
rs12146709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12303852	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs12368923	0.86[ASN][1000 genomes]
rs12369125	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12370947	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12579616	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12809355	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12825440	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12826615	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12830910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241828	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278558	0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2289302	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304630	0.84[JPT][hapmap]
rs35133495	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35336533	0.86[ASN][1000 genomes]
rs36074842	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4082413	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs4335626	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59177896	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61923728	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487928	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487934	0.86[ASN][1000 genomes]
rs6487936	0.86[ASN][1000 genomes]
rs6487939	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7299800	0.86[ASN][1000 genomes]
rs7304221	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7952744	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7955804	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957141	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7958274	0.83[ASN][1000 genomes]
rs7958276	0.85[ASN][1000 genomes]
rs7966063	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971762	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7971870	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7978343	0.85[CEU][hapmap]
rs7979718	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980510	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12809335	IPO8	cis	Artery Tibial	GTEx
rs12809335	IPO8	cis	cerebellum	SCAN
rs12809335	IPO8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30846400-30849400	Active TSS	Rectal Smooth Muscle	rectum
2	chr12:30846800-30849400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:30847000-30849000	Active TSS	Muscle Satellite Cultured Cells	--
4	chr12:30847200-30849000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:30847400-30849000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr12:30847400-30849200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:30847400-30849200	Active TSS	Fetal Intestine Small	intestine
8	chr12:30847400-30849200	Active TSS	Lung	lung
9	chr12:30847400-30849200	Active TSS	Pancreas	Pancrea
10	chr12:30847400-30849400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:30847400-30849400	Active TSS	Aorta	Aorta
12	chr12:30847400-30849400	Active TSS	Fetal Muscle Trunk	muscle
13	chr12:30847400-30849400	Active TSS	Right Atrium	heart
14	chr12:30847400-30849400	Active TSS	GM12878-XiMat	blood
15	chr12:30847400-30849800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr12:30847400-30849800	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr12:30847400-30850400	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr12:30847600-30848800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:30847600-30849000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:30847600-30849000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:30847600-30849200	Active TSS	Left Ventricle	heart
22	chr12:30847600-30849200	Active TSS	Right Ventricle	heart
23	chr12:30847600-30849200	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr12:30847600-30849400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:30847600-30849400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:30847600-30849400	Active TSS	Brain Anterior Caudate	brain
27	chr12:30847600-30849400	Active TSS	Fetal Intestine Large	intestine
28	chr12:30847600-30849400	Active TSS	Ovary	ovary
29	chr12:30847600-30849400	Active TSS	NHDF-Ad	bronchial
30	chr12:30847600-30849600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:30847600-30849600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:30847600-30849600	Active TSS	Colonic Mucosa	Colon
33	chr12:30847600-30849600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr12:30847600-30849600	Active TSS	NHLF	lung
35	chr12:30847600-30849800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr12:30847600-30849800	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr12:30847600-30849800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:30847600-30849800	Active TSS	Duodenum Mucosa	Duodenum
39	chr12:30847800-30849000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr12:30847800-30849000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:30847800-30849000	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr12:30847800-30849000	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr12:30847800-30849000	Active TSS	Fetal Kidney	kidney
44	chr12:30847800-30849000	Active TSS	Fetal Muscle Leg	muscle
45	chr12:30847800-30849000	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr12:30847800-30849000	Active TSS	Hela-S3	cervix
47	chr12:30847800-30849000	Active TSS	HMEC	breast
48	chr12:30847800-30849000	Active TSS	Osteobl	bone
49	chr12:30847800-30849200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:30847800-30849200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links