Variant report

Variant	rs12472081
Chromosome Location	chr2:191398545-191398546
allele	A/G
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	POLR2A	chr2:191398432-191399945	GM12892	blood:	n/a	n/a
2	CREB1	chr2:191398487-191400032	HepG2	liver:	n/a	n/a
3	RCOR1	chr2:191398537-191399781	HepG2	liver:	n/a	n/a
4	USF2	chr2:191398237-191399549	GM12878	blood:	n/a	chr2:191398742-191398753
5	POLR2A	chr2:191398519-191399978	HepG2	liver:	n/a	n/a
6	JUND	chr2:191398341-191398697	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:191398545-191399782	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:191398351-191399847	GM12878	blood:	n/a	n/a
9	YY1	chr2:191398501-191399822	GM12891	blood:	n/a	chr2:191399468-191399477 chr2:191399560-191399574 chr2:191399554-191399568
10	MAX	chr2:191398480-191400024	MCF-7	breast:	n/a	chr2:191399561-191399571
11	CHD1	chr2:191397854-191400364	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:191398458-191399927	GM19193	blood:	n/a	n/a
13	POLR2A	chr2:191398303-191400063	GM12892	blood:	n/a	n/a
14	MYC	chr2:191398367-191399930	NB4	blood:	n/a	chr2:191399561-191399571
15	E2F6	chr2:191398505-191399943	A549	lung:	n/a	chr2:191399494-191399501 chr2:191399204-191399218 chr2:191399207-191399221 chr2:191399494-191399501 chr2:191399124-191399133 chr2:191399128-191399138 chr2:191399490-191399502 chr2:191399494-191399501 chr2:191399510-191399519
16	MYBL2	chr2:191398392-191400077	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:191398318-191400015	GM12892	blood:	n/a	n/a
18	POLR2A	chr2:191398466-191399872	GM12891	blood:	n/a	n/a
19	JUND	chr2:191398148-191399030	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:191398467-191399907	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:191398508-191398831	K562	blood:	n/a	n/a
22	HDAC2	chr2:191398526-191399792	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:191398256-191400006	Raji	blood:	n/a	n/a
24	POLR2A	chr2:191398424-191399925	GM15510	blood:	n/a	n/a
25	POLR2A	chr2:191398449-191399931	GM12891	blood:	n/a	n/a
26	MAX	chr2:191398534-191399893	HepG2	liver:	n/a	chr2:191399561-191399571
27	POLR2A	chr2:191398449-191399977	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr2:191398484-191399897	NB4	blood:	n/a	n/a
29	POLR2A	chr2:191398473-191399939	GM12892	blood:	n/a	n/a
30	POLR2A	chr2:191398518-191399826	SK-N-MC	brain:	n/a	n/a
31	TBP	chr2:191398510-191399952	GM12878	blood:	n/a	n/a
32	NFIC	chr2:191398413-191399990	GM12878	blood:	n/a	n/a
33	RUNX3	chr2:191398117-191399964	GM12878	blood:	n/a	n/a
34	RUNX3	chr2:191398490-191399962	GM12878	blood:	n/a	n/a
35	MAX	chr2:191398277-191400033	NB4	blood:	n/a	chr2:191399561-191399571
36	ATF2	chr2:191398446-191399955	GM12878	blood:	n/a	n/a
37	POLR2A	chr2:191397873-191400077	GM12878	blood:	n/a	n/a
38	POLR2A	chr2:191398214-191399817	GM12878	blood:	n/a	n/a
39	EP300	chr2:191398500-191399876	HepG2	liver:	n/a	chr2:191399551-191399567 chr2:191398501-191398515 chr2:191398507-191398521
40	POLR2A	chr2:191398158-191399977	GM12878	blood:	n/a	n/a
41	MAX	chr2:191398452-191399949	HepG2	liver:	n/a	chr2:191399561-191399571
42	RELA	chr2:191398239-191399896	GM19099	blood:	n/a	n/a
43	POLR2A	chr2:191398484-191399936	GM18505	blood:	n/a	n/a
44	RELA	chr2:191398303-191399837	GM15510	blood:	n/a	n/a
45	HEY1	chr2:191398232-191399944	HepG2	liver:	n/a	n/a
46	FOXA1	chr2:191398465-191399785	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:191398290-191400473	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr2:191398462-191399908	HL-60	blood:	n/a	n/a
49	ATF2	chr2:191398544-191399158	GM12878	blood:	n/a	n/a
50	EBF1	chr2:191398431-191399913	GM12878	blood:	n/a	chr2:191399412-191399423

No.	Distal block	Cell Line	Cell type
1	chr2:191397602..191400323-chr2:191511853..191515845,7	MCF-7	breast:
2	chr10:28821440..28822290-chr2:191398453..191399166,2	NB4	blood:
3	chr2:191397324..191399612-chr2:191415383..191418342,2	MCF-7	breast:
4	chr2:191397736..191401145-chr2:191512338..191515436,3	K562	blood:
5	chr2:191271812..191274120-chr2:191398223..191400840,2	K562	blood:
6	chr2:191385869..191388991-chr2:191394619..191398567,3	K562	blood:
7	chr2:191389345..191393382-chr2:191397304..191400533,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233654	TF binding region
ENSG00000095787	Chromatin interaction
ENSG00000189362	Chromatin interaction
ENSG00000251935	Chromatin interaction
ENSG00000138386	Chromatin interaction
ENSG00000254635	Chromatin interaction
ENSG00000151690	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10174174	0.80[ASN][1000 genomes]
rs10188341	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs10190082	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10197348	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs10432434	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10931458	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1128723	0.90[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11885992	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12052514	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12053190	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12470863	0.81[ASN][1000 genomes]
rs12476782	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12477369	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12693579	0.94[ASN][1000 genomes]
rs16832765	0.92[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2192010	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35818159	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129082	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4258824	0.90[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4261750	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs4287794	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4340549	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4371384	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4439990	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4641969	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4853510	0.96[ASN][1000 genomes]
rs4853710	0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4853713	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4853716	0.95[ASN][1000 genomes]
rs56342910	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58568707	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59929070	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs60915953	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62180992	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62181016	0.85[EUR][1000 genomes]
rs62181018	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62181019	0.85[ASN][1000 genomes]
rs62181020	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62181029	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62181034	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62181052	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62182865	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62182885	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62182897	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62182899	0.82[AFR][1000 genomes]
rs6712426	0.95[ASN][1000 genomes]
rs6727669	0.95[ASN][1000 genomes]
rs6731287	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7567059	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7569128	0.90[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7581762	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7581986	0.87[CHD][hapmap];0.95[JPT][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12472081	HIBCH	cis	cerebellum	SCAN
rs12472081	HIBCH	cis	parietal	SCAN
rs12472081	MFSD6	cis	cerebellum	SCAN
rs12472081	INPP1	Cis_1M	lymphoblastoid	RTeQTL
rs12472081	INPP1	cis	cerebellum	SCAN
rs12472081	INPP1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191375200-191398600	Weak transcription	Ovary	ovary
2	chr2:191387400-191398600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:191391200-191398600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:191393200-191398600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:191393400-191398600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:191393400-191398600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:191393400-191398600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:191393600-191398600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:191394800-191398600	Weak transcription	Esophagus	oesophagus
10	chr2:191394800-191398600	Weak transcription	Gastric	stomach
11	chr2:191395400-191398600	Weak transcription	HSMMtube	muscle
12	chr2:191395600-191398600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:191396200-191398600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:191396200-191398600	Weak transcription	Left Ventricle	heart
15	chr2:191397000-191398600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:191397000-191398600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr2:191397200-191398600	Enhancers	Fetal Heart	heart
18	chr2:191397400-191398600	Flanking Active TSS	Dnd41	blood
19	chr2:191397400-191398800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr2:191397400-191399000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:191397600-191398600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:191397800-191398800	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr2:191397800-191399000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr2:191397800-191401000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr2:191398000-191398600	Enhancers	Placenta	Placenta
26	chr2:191398000-191398800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr2:191398000-191398800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr2:191398000-191399000	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr2:191398000-191399000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:191398000-191399000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr2:191398000-191399000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:191398000-191401000	Active TSS	GM12878-XiMat	blood
33	chr2:191398200-191398600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:191398200-191398600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:191398200-191398600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:191398200-191398600	Enhancers	Pancreas	Pancrea
37	chr2:191398200-191398600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr2:191398200-191398600	Flanking Active TSS	HepG2	liver
39	chr2:191398200-191398800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:191398200-191398800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr2:191398200-191398800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:191398200-191398800	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr2:191398200-191398800	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr2:191398200-191398800	Flanking Active TSS	Fetal Kidney	kidney
45	chr2:191398200-191398800	Flanking Active TSS	Fetal Lung	lung
46	chr2:191398200-191398800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr2:191398200-191398800	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr2:191398200-191398800	Flanking Active TSS	Thymus	Thymus
49	chr2:191398200-191398800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr2:191398200-191399000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links