Variant report

Variant	rs1445498
Chromosome Location	chr11:85526690-85526691
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	TCF12	chr11:85525759-85527064	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr11:85526014-85526877	SK-N-SH	brain:	n/a	n/a
5	MAX	chr11:85526122-85526857	SK-N-SH	brain:	n/a	n/a
6	EP300	chr11:85525910-85527044	SK-N-SH	brain:	n/a	chr11:85526242-85526256
7	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
8	RXRA	chr11:85526060-85527037	SK-N-SH	brain:	n/a	n/a
9	PBX3	chr11:85525906-85527065	SK-N-SH	brain:	n/a	n/a
10	EP300	chr11:85526087-85526888	SK-N-SH_RA	brain:	n/a	chr11:85526242-85526256
11	NFIC	chr11:85525770-85527136	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr11:85525917-85527105	SK-N-SH	brain:	n/a	n/a
13	TEAD4	chr11:85525919-85527052	SK-N-SH	brain:	n/a	n/a
14	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
15	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
16	FOS	chr11:85526171-85526988	MCF10A-Er-Src	breast:	n/a	chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526442-85526450
17	GATA3	chr11:85525818-85527028	SK-N-SH	brain:	n/a	n/a
18	FOS	chr11:85526227-85527058	MCF10A-Er-Src	breast:	n/a	chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526441-85526451 chr11:85526442-85526450
19	EP300	chr11:85526508-85526836	SK-N-SH_RA	brain:	n/a	n/a
20	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
21	GATA3	chr11:85526315-85526705	SH-SY5Y	brain:	n/a	n/a
22	TEAD4	chr11:85526013-85527027	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr11:85526150-85526836	IMR90	lung:	n/a	n/a
24	TCF7L2	chr11:85526283-85526937	HCT-116	colon:	n/a	chr11:85526442-85526451
25	GATA3	chr11:85525866-85527246	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85505294..85507043-chr11:85526404..85527937,2	K562	blood:
2	chr11:85373159..85375270-chr11:85526178..85528131,2	MCF-7	breast:

Variant related genes	Relation type
SYTL2	TF binding region
ENSG00000137504	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11826218	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12361800	0.81[CEU][hapmap]
rs1445500	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1445501	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445505	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445511	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17743946	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17744675	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17744699	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17744711	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17817230	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17817254	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17817308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17817314	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17817326	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17817331	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17817343	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17817355	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2044390	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs36093844	0.81[CEU][hapmap]
rs4296062	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7102361	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7116742	1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7121363	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7127477	1.00[JPT][hapmap]
rs7931771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7943104	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs895256	0.85[AMR][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1445498	SYTL2	cis	lymphoblastoid	seeQTL
rs1445498	CCDC83	cis	parietal	SCAN
rs1445498	FZD4	cis	cerebellum	SCAN
rs1445498	RAB30	cis	cerebellum	SCAN
rs1445498	SYTL2	cis	cerebellum	SCAN
rs1445498	ME3	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr11:85523400-85528400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:85523800-85526800	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr11:85524400-85532600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr11:85524800-85527800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:85524800-85537200	Weak transcription	Small Intestine	intestine
8	chr11:85525000-85528400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:85525000-85529000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:85525200-85528400	Enhancers	NHLF	lung
11	chr11:85525200-85528800	Enhancers	NHDF-Ad	bronchial
12	chr11:85525200-85529600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr11:85525400-85527600	Enhancers	Osteobl	bone
14	chr11:85525600-85526800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:85525600-85527200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:85525600-85528000	Enhancers	HSMM	muscle
17	chr11:85525600-85530000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr11:85525800-85526800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:85525800-85526800	Enhancers	NH-A	brain
20	chr11:85525800-85527000	Enhancers	HMEC	breast
21	chr11:85525800-85527200	Enhancers	NHEK	skin
22	chr11:85525800-85527400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:85525800-85527600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:85526000-85526800	Enhancers	A549	lung
25	chr11:85526200-85526800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:85526200-85526800	Enhancers	Primary T cells from cord blood	blood
27	chr11:85526400-85526800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:85526600-85526800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:85526600-85527000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:85526600-85527000	Enhancers	Primary T helper cells fromperipheralblood	blood

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