Variant report

Variant	rs632632
Chromosome Location	chr2:136638216-136638217
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	CEBPB	chr2:136638129-136638438	HepG2	liver:	n/a	chr2:136638294-136638305
2	CEBPB	chr2:136638202-136638436	A549	lung:	n/a	chr2:136638294-136638305
3	CEBPB	chr2:136638148-136638433	K562	blood:	n/a	chr2:136638294-136638305

No.	Distal block	Cell Line	Cell type
1	chr2:136637552..136640053-chr2:136741843..136744426,2	K562	blood:
2	chr2:136637310..136640053-chr2:136741843..136745319,3	K562	blood:
3	chr2:136637180..136639583-chr2:136640234..136642830,2	K562	blood:

Variant related genes	Relation type
MCM6	TF binding region
ENSG00000115866	Chromatin interaction
ENSG00000231890	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1011361	1.00[CHB][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs10186843	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10188066	0.80[MEX][hapmap]
rs10202489	1.00[ASW][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.92[MEX][hapmap];0.82[YRI][hapmap]
rs10207652	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11679508	0.82[YRI][hapmap]
rs11684545	1.00[CHB][hapmap]
rs12185712	0.93[CEU][hapmap]
rs12615624	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs12620033	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12988076	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12994270	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs12998387	1.00[CHB][hapmap]
rs13404551	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1435576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438305	0.95[CHB][hapmap];0.82[YRI][hapmap]
rs1438307	1.00[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.82[YRI][hapmap]
rs1470457	0.81[EUR][1000 genomes]
rs160329	0.91[EUR][1000 genomes]
rs188680	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs192822	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2164210	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs218174	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236783	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278544	0.88[MEX][hapmap]
rs2322659	0.83[MEX][hapmap]
rs2322660	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2322818	0.84[EUR][1000 genomes]
rs309125	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309128	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs309130	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs309134	0.83[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap]
rs309137	0.82[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes]
rs309145	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309160	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309164	0.83[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs309168	0.82[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs309173	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs309176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs309178	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs309179	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs309180	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs309181	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs309811	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs313518	0.91[ASW][hapmap];0.83[CEU][hapmap];0.82[YRI][hapmap]
rs313519	0.83[CEU][hapmap]
rs313526	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs313528	0.90[ASW][hapmap];0.82[CEU][hapmap];0.82[YRI][hapmap]
rs3213889	1.00[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.82[YRI][hapmap]
rs3739020	0.82[EUR][1000 genomes]
rs3754686	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769005	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4954450	0.84[EUR][1000 genomes]
rs4954490	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4954493	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4988183	0.84[EUR][1000 genomes]
rs4988226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55830620	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62159034	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6430589	0.83[EUR][1000 genomes]
rs666407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719488	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes]
rs6730196	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6742283	0.93[EUR][1000 genomes]
rs6754311	0.80[CEU][hapmap]
rs680428	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs687670	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7355359	0.82[CEU][hapmap]
rs745500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs748841	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7569057	0.94[EUR][1000 genomes]
rs7579771	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs892715	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[EUR][1000 genomes]
rs9287442	0.81[CHB][hapmap];0.88[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv960989	chr2:136636095-136649068	Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs632632	MCM6	cis	cerebellum	SCAN
rs632632	R3HDM1	cis	cerebellum	SCAN
rs632632	MCM6	cis	Artery Tibial	GTEx
rs632632	MCM6	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:136634200-136641200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:136634600-136639600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:136634800-136639400	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links