Variant report

Variant	rs12623588
Chromosome Location	chr2:10957612-10957613
allele	C/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	RAD21	chr2:10957588-10957950	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr2:10957580-10957730	AG09319	gingival:	n/a	chr2:10957702-10957711
3	MYC	chr2:10957578-10957713	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr2:10957560-10957710	GM12865	blood:	n/a	n/a
5	CTCF	chr2:10957595-10957825	HepG2	liver:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
6	CTCF	chr2:10957585-10957847	H1-hESC	embryonic stem cell:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
7	CTCF	chr2:10957580-10957730	BJ	skin:	n/a	chr2:10957702-10957711
8	EP300	chr2:10957577-10957714	HepG2	liver:	n/a	n/a
9	CTCF	chr2:10957600-10957750	AG04450	lung:	n/a	chr2:10957702-10957711
10	CTCF	chr2:10957521-10957906	H1-hESC	embryonic stem cell:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
11	CTCF	chr2:10957547-10957880	IMR90	lung:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
12	CTCF	chr2:10957560-10957710	GM12864	blood:	n/a	n/a
13	CTCF	chr2:10957295-10958035	SK-N-SH	brain:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
14	CTCF	chr2:10957540-10957690	HRE	kidney:	n/a	n/a
15	CTCF	chr2:10957520-10957670	HAc	cerebellar:	n/a	n/a
16	CTCF	chr2:10957326-10957913	A549	lung:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
17	RAD21	chr2:10957515-10957840	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr2:10957500-10957650	A549	lung:	n/a	n/a
19	CTCF	chr2:10957605-10957810	GM19238	blood:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
20	CTCF	chr2:10957509-10957906	MCF-7	breast:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
21	CTCF	chr2:10957600-10957750	GM06990	blood:	n/a	chr2:10957702-10957711
22	CTCF	chr2:10957606-10957834	H1-hESC	embryonic stem cell:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
23	SIN3A	chr2:10957562-10957815	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr2:10957594-10957770	T-47D	breast:	n/a	chr2:10957702-10957711
25	RAD21	chr2:10957582-10957803	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr2:10957505-10957793	HepG2	liver:	n/a	chr2:10957702-10957711
27	RAD21	chr2:10957567-10957763	HepG2	liver:	n/a	n/a
28	CTCF	chr2:10957550-10957791	SK-N-SH_RA	brain:	n/a	chr2:10957702-10957711
29	CTCF	chr2:10957580-10957730	GM12873	blood:	n/a	chr2:10957702-10957711
30	RAD21	chr2:10957591-10957878	HepG2	liver:	n/a	n/a
31	CTCF	chr2:10957607-10957792	HUVEC	blood vessel:	n/a	chr2:10957702-10957711
32	RAD21	chr2:10957579-10957809	HepG2	liver:	n/a	n/a
33	CTCF	chr2:10957580-10957730	HEK293	kidney:	n/a	chr2:10957702-10957711
34	CTCF	chr2:10957520-10957670	WI-38	lung:	n/a	n/a
35	CTCF	chr2:10957600-10957750	GM12871	blood:	n/a	chr2:10957702-10957711
36	CTCF	chr2:10957600-10957750	AoAF	blood vessel:	n/a	chr2:10957702-10957711
37	ZNF143	chr2:10957556-10957856	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr2:10957593-10957828	SK-N-SH_RA	brain:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
39	CTCF	chr2:10957611-10957825	Gliobla	brain:	n/a	chr2:10957786-10957795 chr2:10957702-10957711
40	RAD21	chr2:10957576-10957778	SK-N-SH_RA	brain:	n/a	n/a
41	CHD1	chr2:10957577-10957628	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr2:10957569-10957791	A549	lung:	n/a	chr2:10957702-10957711
43	SMC3	chr2:10957580-10957773	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10951755..10953479-chr2:10956167..10958157,2	K562	blood:

Variant related genes	Relation type
RNU7-176P	TF binding region
PDIA6	TF binding region
ENSG00000143870	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10192112	0.83[AFR][1000 genomes]
rs10197595	0.88[LWK][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs10200007	0.84[AFR][1000 genomes]
rs1198844	0.94[CHD][hapmap]
rs12463454	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12471725	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs12471762	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs12472302	0.81[ASN][1000 genomes]
rs12474895	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475790	0.91[ASN][1000 genomes]
rs12621237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404780	0.88[LWK][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs13429247	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13431633	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13431852	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13432104	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17365181	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs17365209	0.81[ASN][1000 genomes]
rs17365216	0.81[ASN][1000 genomes]
rs17455708	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17456162	0.81[ASN][1000 genomes]
rs17456225	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306922	0.81[ASN][1000 genomes]
rs2357815	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2357816	0.84[AFR][1000 genomes]
rs2884289	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3856465	0.92[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55648622	0.81[ASN][1000 genomes]
rs55688940	0.81[ASN][1000 genomes]
rs55770944	0.81[ASN][1000 genomes]
rs55771723	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55968911	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55975412	0.91[ASN][1000 genomes]
rs56025654	0.81[ASN][1000 genomes]
rs56093996	0.81[ASN][1000 genomes]
rs56121730	0.81[ASN][1000 genomes]
rs56140102	0.81[ASN][1000 genomes]
rs56141717	0.81[ASN][1000 genomes]
rs56147885	0.81[ASN][1000 genomes]
rs56162318	0.81[ASN][1000 genomes]
rs56260452	0.91[ASN][1000 genomes]
rs56263234	0.81[ASN][1000 genomes]
rs56264212	0.81[ASN][1000 genomes]
rs56268818	0.91[ASN][1000 genomes]
rs56321198	0.81[ASN][1000 genomes]
rs56344711	0.81[ASN][1000 genomes]
rs59737886	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72779425	0.81[ASN][1000 genomes]
rs72779433	0.81[ASN][1000 genomes]
rs72779445	0.91[ASN][1000 genomes]
rs72779451	0.81[ASN][1000 genomes]
rs72779452	0.81[ASN][1000 genomes]
rs72779453	0.81[ASN][1000 genomes]
rs72779459	0.81[ASN][1000 genomes]
rs72779464	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72779466	0.81[ASN][1000 genomes]
rs72779469	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72779470	0.81[ASN][1000 genomes]
rs72779474	0.81[ASN][1000 genomes]
rs72779478	0.81[ASN][1000 genomes]
rs7571007	0.81[ASN][1000 genomes]
rs7576898	0.84[CEU][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7587453	0.81[ASN][1000 genomes]
rs7590368	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12623588	ODC1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10953600-10957800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:10953600-10959200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:10953600-10960800	Weak transcription	Brain Substantia Nigra	brain
4	chr2:10953600-10960800	Weak transcription	Left Ventricle	heart
5	chr2:10953600-10968200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:10953800-10960800	Weak transcription	Spleen	Spleen
7	chr2:10955000-10960600	Weak transcription	Stomach Mucosa	stomach
8	chr2:10955200-10958600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:10955400-10958800	Weak transcription	HUVEC	blood vessel
10	chr2:10955400-10968600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:10955600-10960800	Weak transcription	Adipose Nuclei	Adipose
12	chr2:10957600-10957800	Bivalent Enhancer	Hela-S3	cervix
13	chr2:10957600-10959000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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