Variant report

Variant	rs2736542
Chromosome Location	chr11:5402657-5402658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:5398331-5406514..11:5707362-5712027	K562	blood:
2	chr11:5225752..5226648-chr11:5401460..5402799,4	MCF-7	breast:
3	chr11:5402164..5402741-chr11:5497230..5497968,2	MCF-7	breast:
4	11:5243048-5250847..11:5398331-5406514	H1-hESC	embryonic stem cell:	embryo
5	11:5250847-5268367..11:5398331-5406514	Hela-S3	cervix:
6	11:5398331-5406514..11:5527719-5533869	H1-hESC	embryonic stem cell:	embryo
7	11:4778081-4789138..11:5398331-5406514	Hela-S3	cervix:
8	11:5398331-5406514..11:5700314-5707362	GM12878	blood:
9	11:5146608-5154908..11:5398331-5406514	GM12878	blood:
10	11:5018576-5020673..11:5398331-5406514	H1-hESC	embryonic stem cell:	embryo
11	11:5218976-5222789..11:5398331-5406514	GM12878	blood:

No data

Variant related genes	Relation type
ENSG00000244734	Chromatin interaction
ENSG00000223609	Chromatin interaction
ENSG00000224091	Chromatin interaction
ENSG00000171944	Chromatin interaction
ENSG00000176742	Chromatin interaction
ENSG00000260629	Chromatin interaction
ENSG00000132274	Chromatin interaction
ENSG00000175520	Chromatin interaction
ENSG00000229988	Chromatin interaction
ENSG00000132256	Chromatin interaction
ENSG00000221031	Chromatin interaction
ENSG00000167346	Chromatin interaction
ENSG00000176798	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10500638	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs10768920	0.80[YRI][hapmap]
rs11037049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11037127	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12802177	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1498472	0.85[YRI][hapmap]
rs1546216	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs1846318	0.85[EUR][1000 genomes]
rs2340655	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2647546	0.93[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs2647549	0.93[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs2647557	0.93[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs2647583	0.81[YRI][hapmap]
rs2647610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2723372	0.93[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs2723373	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2723379	0.85[EUR][1000 genomes]
rs2736521	0.80[YRI][hapmap]
rs2736530	0.89[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs2736533	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs2736534	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs2736536	0.93[CEU][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs2736547	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2736548	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2975552	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34474660	0.90[ASN][1000 genomes]
rs4910769	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910773	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs5024041	0.89[CEU][hapmap]
rs6578642	0.80[YRI][hapmap]
rs7113335	0.91[CEU][hapmap]
rs7116499	0.93[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs872163	0.81[YRI][hapmap]
rs872166	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524400	chr11:5328361-5416622	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
3	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv896931	chr11:5357881-5505149	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv832057	chr11:5375585-5576200	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv896932	chr11:5392484-5424170	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
7	nsv1044243	chr11:5401036-5432316	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	nsv896933	chr11:5402315-5440620	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2736542	TRIM68	cis	parietal	SCAN
rs2736542	OR52E4	cis	cerebellum	SCAN
rs2736542	KRTAP5-2	cis	cerebellum	SCAN
rs2736542	OR52H1	cis	cerebellum	SCAN
rs2736542	OR51B2	cis	cerebellum	SCAN
rs2736542	MOB2	cis	cerebellum	SCAN
rs2736542	TRIM66	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5401000-5404400	Strong transcription	K562	blood
2	chr11:5402400-5405000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links