Variant report

Variant	rs10878161
Chromosome Location	chr12:40546554-40546555
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	CTCF	chr12:40546552-40546989	A549	lung:	n/a	chr12:40546776-40546792 chr12:40546777-40546798 chr12:40546778-40546791 chr12:40546775-40546793
2	RAD21	chr12:40546484-40547110	MCF-7	breast:	n/a	chr12:40546776-40546795
3	CTCF	chr12:40546212-40547681	A549	lung:	n/a	chr12:40546776-40546792 chr12:40546777-40546798 chr12:40546778-40546791 chr12:40546775-40546793
4	RAD21	chr12:40546539-40546968	Hela-S3	cervix:	n/a	chr12:40546776-40546795
5	CTCF	chr12:40546532-40546974	GM12878	blood:	n/a	chr12:40546776-40546792 chr12:40546777-40546798 chr12:40546778-40546791 chr12:40546775-40546793
6	RAD21	chr12:40546500-40546999	A549	lung:	n/a	chr12:40546776-40546795
7	CTCF	chr12:40546404-40547176	SK-N-SH	brain:	n/a	chr12:40546776-40546792 chr12:40546777-40546798 chr12:40546778-40546791 chr12:40546775-40546793
8	RAD21	chr12:40546481-40547050	A549	lung:	n/a	chr12:40546776-40546795
9	RAD21	chr12:40546527-40547005	ECC-1	luminal epithelium:	n/a	chr12:40546776-40546795
10	FOXM1	chr12:40546529-40546974	GM12878	blood:	n/a	n/a
11	CTCF	chr12:40546507-40547046	MCF-7	breast:	n/a	chr12:40546776-40546792 chr12:40546777-40546798 chr12:40546778-40546791 chr12:40546775-40546793
12	POU2F2	chr12:40546493-40546862	GM12878	blood:	n/a	chr12:40546747-40546760
13	CTCF	chr12:40546550-40546956	HepG2	liver:	n/a	chr12:40546776-40546792 chr12:40546777-40546798 chr12:40546778-40546791 chr12:40546775-40546793
14	CTCF	chr12:40546499-40546971	T-47D	breast:	n/a	chr12:40546776-40546792 chr12:40546777-40546798 chr12:40546778-40546791 chr12:40546775-40546793
15	RAD21	chr12:40546540-40547066	MCF-7	breast:	n/a	chr12:40546776-40546795
16	RAD21	chr12:40546519-40546975	SK-N-SH_RA	brain:	n/a	chr12:40546776-40546795
17	RAD21	chr12:40546475-40546979	HCT-116	colon:	n/a	chr12:40546776-40546795
18	RAD21	chr12:40546365-40547250	SK-N-SH	brain:	n/a	chr12:40546776-40546795

No.	Distal block	Cell Line	Cell type
1	chr12:40536767..40538493-chr12:40545018..40546756,2	K562	blood:
2	12:40545640-40549031..12:40691796-40694737	GM12878	blood:
3	chr12:40546299..40547451-chr12:40706483..40707430,5	MCF-7	breast:
4	chr12:40546325..40546967-chr12:40662693..40663558,3	MCF-7	breast:
5	chr12:40158520..40159448-chr12:40546284..40547792,5	MCF-7	breast:
6	chr12:40546236..40547437-chr12:40706403..40707441,12	MCF-7	breast:
7	12:40545640-40549031..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000223914	TF binding region
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10437933	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10437934	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784407	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878160	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878162	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878170	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878174	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878180	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878199	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11612806	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1463721	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442770	0.94[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307016	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708418	0.80[ASN][1000 genomes]
rs2708420	0.81[ASN][1000 genomes]
rs2708422	0.81[ASN][1000 genomes]
rs2708435	0.86[JPT][hapmap]
rs4567538	0.86[JPT][hapmap]
rs6581578	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7307584	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs767940	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7969112	0.84[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10878161	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40541400-40546600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr12:40541800-40546600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr12:40543800-40547200	Weak transcription	HMEC	breast
4	chr12:40544000-40547400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:40544200-40546600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:40544200-40546600	Weak transcription	A549	lung
7	chr12:40544200-40547000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:40544200-40547200	Weak transcription	NHEK	skin
9	chr12:40546200-40547400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links