Variant report

Variant	rs11607789
Chromosome Location	chr11:85526151-85526152
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	EP300	chr11:85525932-85527175	SK-N-SH	brain:	n/a	chr11:85526242-85526256
2	PBX3	chr11:85525818-85527087	SK-N-SH	brain:	n/a	n/a
3	E2F4	chr11:85526149-85526502	MCF10A-Er-Src	breast:	n/a	n/a
4	TCF12	chr11:85525759-85527064	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr11:85526014-85526877	SK-N-SH	brain:	n/a	n/a
6	MAX	chr11:85526122-85526857	SK-N-SH	brain:	n/a	n/a
7	EP300	chr11:85525910-85527044	SK-N-SH	brain:	n/a	chr11:85526242-85526256
8	FOSL2	chr11:85526061-85527072	SK-N-SH	brain:	n/a	chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526442-85526450
9	RXRA	chr11:85526060-85527037	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr11:85525906-85527065	SK-N-SH	brain:	n/a	n/a
11	MAFK	chr11:85526043-85526492	IMR90	lung:	n/a	n/a
12	EP300	chr11:85526087-85526888	SK-N-SH_RA	brain:	n/a	chr11:85526242-85526256
13	NFIC	chr11:85525770-85527136	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr11:85525917-85527105	SK-N-SH	brain:	n/a	n/a
15	TEAD4	chr11:85525919-85527052	SK-N-SH	brain:	n/a	n/a
16	JUND	chr11:85525950-85527089	SK-N-SH	brain:	n/a	chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526442-85526450
17	FOSL2	chr11:85525884-85527061	SK-N-SH	brain:	n/a	chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526442-85526450
18	GATA3	chr11:85525818-85527028	SK-N-SH	brain:	n/a	n/a
19	JUND	chr11:85526024-85527059	SK-N-SH	brain:	n/a	chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526442-85526450
20	TEAD4	chr11:85526013-85527027	SK-N-SH	brain:	n/a	n/a
21	CEBPB	chr11:85526150-85526836	IMR90	lung:	n/a	n/a
22	GATA3	chr11:85525866-85527246	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
SYTL2	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11234388	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs11234389	0.85[CHB][hapmap]
rs11234391	0.85[CHB][hapmap]
rs11234393	0.85[CHB][hapmap]
rs11234397	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs11606656	0.85[YRI][hapmap]
rs17148355	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs17148514	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17208525	0.85[CHB][hapmap]
rs17208602	0.85[CHB][hapmap]
rs17208616	0.85[CHB][hapmap]
rs17810701	0.85[CHB][hapmap]
rs17810766	0.85[CHB][hapmap]
rs17810802	0.85[CHB][hapmap]
rs17810855	0.85[CHB][hapmap]
rs17811120	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs2044393	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs2276018	0.85[CHB][hapmap]
rs2304342	0.85[CHB][hapmap]
rs678376	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1047147	chr11:85459235-85594800	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv541114	chr11:85459235-85594800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv2762927	chr11:85468051-85559618	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1052737	chr11:85477084-85554914	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv541115	chr11:85477084-85554914	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1049630	chr11:85486866-85535123	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
13	nsv1048818	chr11:85524635-85746473	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	nsv541116	chr11:85524635-85746473	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11607789	GRM5	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85522600-85527000	Enhancers	Stomach Mucosa	stomach
2	chr11:85522600-85533200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:85522800-85526200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr11:85522800-85526200	Weak transcription	Primary T cells from cord blood	blood
5	chr11:85522800-85526200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr11:85523000-85526600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:85523000-85526600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr11:85523000-85526600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:85523400-85528400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:85523800-85526200	Enhancers	Duodenum Mucosa	Duodenum
11	chr11:85523800-85526800	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr11:85524400-85532600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr11:85524600-85526600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:85524800-85527800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:85524800-85537200	Weak transcription	Small Intestine	intestine
16	chr11:85525000-85528400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:85525000-85529000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:85525200-85528400	Enhancers	NHLF	lung
19	chr11:85525200-85528800	Enhancers	NHDF-Ad	bronchial
20	chr11:85525200-85529600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr11:85525400-85526200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:85525400-85527600	Enhancers	Osteobl	bone
23	chr11:85525600-85526800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:85525600-85527200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:85525600-85528000	Enhancers	HSMM	muscle
26	chr11:85525600-85530000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr11:85525800-85526400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:85525800-85526800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:85525800-85526800	Enhancers	NH-A	brain
30	chr11:85525800-85527000	Enhancers	HMEC	breast
31	chr11:85525800-85527200	Enhancers	NHEK	skin
32	chr11:85525800-85527400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:85525800-85527600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:85526000-85526800	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links