Variant report

Variant	rs2638261
Chromosome Location	chr12:40548697-40548698
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	YY1	chr12:40548623-40548954	H1-hESC	embryonic stem cell:	n/a	chr12:40548794-40548806 chr12:40548795-40548817 chr12:40548797-40548806

No.	Distal block	Cell Line	Cell type	Cell Stage
1	12:40545640-40549031..12:40691796-40694737	GM12878	blood:
2	12:40545640-40549031..12:40703633-40711447	GM12878	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1388585	1.00[YRI][hapmap]
rs2244159	0.90[AFR][1000 genomes]
rs2244534	0.85[YRI][hapmap];1.00[AFR][1000 genomes]
rs2244780	0.85[YRI][hapmap];0.90[AFR][1000 genomes]
rs2253021	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs2253171	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2253867	0.86[AFR][1000 genomes]
rs2638223	0.86[AFR][1000 genomes]
rs2638235	0.85[YRI][hapmap];1.00[AFR][1000 genomes]
rs2638236	1.00[AFR][1000 genomes]
rs2638237	1.00[AFR][1000 genomes]
rs2638240	1.00[AFR][1000 genomes]
rs2638241	0.85[YRI][hapmap];1.00[AFR][1000 genomes]
rs2638242	0.90[AFR][1000 genomes]
rs2638243	0.85[YRI][hapmap];1.00[AFR][1000 genomes]
rs2638265	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2708403	0.83[YRI][hapmap];1.00[AFR][1000 genomes]
rs2708405	0.82[YRI][hapmap];1.00[AFR][1000 genomes]
rs2708406	0.85[YRI][hapmap];1.00[AFR][1000 genomes]
rs2708410	1.00[AFR][1000 genomes]
rs2708411	0.87[AFR][1000 genomes]
rs2708415	1.00[AFR][1000 genomes]
rs2708416	0.85[YRI][hapmap]
rs2708460	0.86[AFR][1000 genomes]
rs2708461	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2708462	1.00[AFR][1000 genomes]
rs2708471	1.00[AFR][1000 genomes]
rs2708475	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2708483	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2708484	1.00[YRI][hapmap];0.93[AFR][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

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40547200-40558600	Weak transcription	Liver	Liver
2	chr12:40547600-40551800	Weak transcription	NHEK	skin
3	chr12:40547800-40549600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr12:40547800-40549600	Weak transcription	GM12878-XiMat	blood
5	chr12:40547800-40551200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:40547800-40551200	Weak transcription	HMEC	breast
7	chr12:40547800-40551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:40547800-40552200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:40548000-40548800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr12:40548000-40549800	Weak transcription	Primary B cells from cord blood	blood
11	chr12:40548400-40548800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr12:40548400-40548800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr12:40548400-40548800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr12:40548400-40549200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr12:40548400-40549400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr12:40548400-40549400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr12:40548400-40549600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:40548400-40549800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:40548400-40551200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:40548600-40549000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr12:40548600-40550200	Enhancers	HUES64 Cell Line	embryonic stem cell

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