Variant report

Variant	rs10838680
Chromosome Location	chr11:5839744-5839745
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	IRF1	chr11:5839721-5839990	K562	blood:	n/a	chr11:5839903-5839917 chr11:5839901-5839911 chr11:5839895-5839909 chr11:5839895-5839912 chr11:5839899-5839919 chr11:5839897-5839911 chr11:5839901-5839915 chr11:5839899-5839910 chr11:5839907-5839917
2	EBF1	chr11:5839416-5840361	GM12878	blood:	n/a	chr11:5839662-5839673 chr11:5839664-5839673 chr11:5839662-5839675 chr11:5839663-5839673 chr11:5839664-5839673
3	STAT3	chr11:5839738-5839753	GM12878	blood:	n/a	n/a
4	EBF1	chr11:5839411-5839898	GM12878	blood:	n/a	chr11:5839662-5839673 chr11:5839664-5839673 chr11:5839662-5839675 chr11:5839663-5839673 chr11:5839664-5839673
5	IRF1	chr11:5839651-5840110	K562	blood:	n/a	chr11:5839903-5839917 chr11:5839901-5839911 chr11:5839895-5839909 chr11:5839895-5839912 chr11:5839899-5839919 chr11:5839897-5839911 chr11:5839901-5839915 chr11:5839899-5839910 chr11:5839907-5839917
6	EBF1	chr11:5839448-5839917	GM12878	blood:	n/a	chr11:5839662-5839673 chr11:5839664-5839673 chr11:5839662-5839675 chr11:5839663-5839673 chr11:5839664-5839673
7	IRF1	chr11:5839497-5840155	K562	blood:	n/a	chr11:5839903-5839917 chr11:5839901-5839911 chr11:5839895-5839909 chr11:5839895-5839912 chr11:5839899-5839919 chr11:5839897-5839911 chr11:5839901-5839915 chr11:5839899-5839910 chr11:5839907-5839917
8	RCOR1	chr11:5839626-5839931	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5831234..5833906-chr11:5837299..5840310,4	K562	blood:
2	chr11:5831234..5833906-chr11:5837299..5840310,3	K562	blood:

Variant related genes	Relation type
OR52N2	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10742794	0.83[EUR][1000 genomes]
rs10769250	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838661	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10838668	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10838672	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838673	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838674	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039085	0.96[ASN][1000 genomes]
rs11039150	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11500473	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12226188	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12279684	0.96[ASN][1000 genomes]
rs35271555	0.96[ASN][1000 genomes]
rs35898746	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57482916	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7112569	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7115498	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7122745	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8181512	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8181529	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9630185	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9630186	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
8	nsv553277	chr11:5722948-6010075	Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv1843296	chr11:5730377-5970717	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	esv2758255	chr11:5730377-5970717	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv2759801	chr11:5730377-6007613	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv832058	chr11:5747594-5926814	Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
13	esv2757421	chr11:5776623-5842356	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv896952	chr11:5832191-5893376	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
15	nsv972956	chr11:5838557-5842082	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10838680	OR52N3P	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5837600-5841200	Weak transcription	K562	blood
2	chr11:5837600-5844600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:5839400-5839800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr11:5839400-5839800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr11:5839400-5840400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr11:5839400-5840400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:5839400-5840400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr11:5839400-5840400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:5839600-5839800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr11:5839600-5839800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr11:5839600-5839800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:5839600-5839800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr11:5839600-5839800	Flanking Active TSS	GM12878-XiMat	blood
14	chr11:5839600-5840000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:5839600-5840000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr11:5839600-5840000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr11:5839600-5840000	Flanking Active TSS	Liver	Liver
18	chr11:5839600-5840000	Active TSS	NHLF	lung
19	chr11:5839600-5840200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr11:5839600-5840200	Active TSS	Duodenum Mucosa	Duodenum
21	chr11:5839600-5840200	Flanking Active TSS	Dnd41	blood
22	chr11:5839600-5840400	Enhancers	Primary B cells from peripheral blood	blood
23	chr11:5839600-5840400	Enhancers	Primary T cells from cord blood	blood
24	chr11:5839600-5840400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr11:5839600-5840400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr11:5839600-5840400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:5839600-5840400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links