Variant report

Variant	rs1783541
Chromosome Location	chr11:65294799-65294800
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	POLR2A	chr11:65294785-65295015	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65292702..65295176-chr11:65381785..65383528,2	MCF-7	breast:
2	chr11:65185186..65203592-chr11:65286522..65299399,55	K562	blood:

Variant related genes	Relation type
SCYL1	TF binding region
ENSG00000245532	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000173327	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10896009	0.91[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs10896012	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap]
rs10896015	0.83[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap]
rs11227199	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs11227217	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1144928	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194076	0.83[JPT][hapmap]
rs12270054	0.83[JPT][hapmap];0.81[MEX][hapmap];0.81[MKK][hapmap]
rs12360896	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs1346	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs17146964	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs1787663	0.90[CEU][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs2846139	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3200401	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap]
rs58621819	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7931311	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs947791	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
4	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
5	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
6	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
7	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
8	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
9	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
10	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
11	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
12	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
13	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases
14	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
15	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
16	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
17	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
18	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1783541	SNX32	cis	parietal	SCAN
rs1783541	LTBP3	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65293400-65296400	Weak transcription	Aorta	Aorta
2	chr11:65293600-65294800	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr11:65293600-65294800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:65293600-65294800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr11:65293600-65295000	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr11:65293600-65297400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:65293600-65297600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:65293600-65297600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr11:65293600-65297800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:65293600-65299000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:65293600-65300200	Weak transcription	Psoas Muscle	Psoas
12	chr11:65293600-65305600	Weak transcription	Right Atrium	heart
13	chr11:65293600-65307600	Weak transcription	Small Intestine	intestine
14	chr11:65293800-65294800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr11:65293800-65294800	Genic enhancers	K562	blood
16	chr11:65293800-65295400	Strong transcription	Fetal Kidney	kidney
17	chr11:65293800-65295600	Genic enhancers	Liver	Liver
18	chr11:65293800-65296000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:65293800-65296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:65293800-65297600	Weak transcription	A549	lung
21	chr11:65293800-65298000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:65293800-65302800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:65294000-65294800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr11:65294000-65294800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:65294000-65294800	Genic enhancers	Pancreas	Pancrea
26	chr11:65294000-65294800	Genic enhancers	Stomach Smooth Muscle	stomach
27	chr11:65294000-65295000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr11:65294000-65295000	Strong transcription	Ovary	ovary
29	chr11:65294000-65295800	Weak transcription	Primary B cells from cord blood	blood
30	chr11:65294000-65296200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:65294000-65296400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:65294000-65296800	Strong transcription	Thymus	Thymus
33	chr11:65294000-65297000	Weak transcription	Left Ventricle	heart
34	chr11:65294000-65297200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:65294000-65297200	Weak transcription	Brain Angular Gyrus	brain
36	chr11:65294000-65298200	Weak transcription	Stomach Mucosa	stomach
37	chr11:65294000-65300200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:65294000-65300600	Strong transcription	HSMM	muscle
39	chr11:65294000-65300800	Strong transcription	Colonic Mucosa	Colon
40	chr11:65294000-65301400	Strong transcription	Esophagus	oesophagus
41	chr11:65294000-65305800	Strong transcription	Fetal Brain Female	brain
42	chr11:65294000-65305800	Strong transcription	Fetal Intestine Large	intestine
43	chr11:65294000-65306400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:65294000-65306400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr11:65294000-65306400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:65294000-65306600	Weak transcription	Fetal Heart	heart
47	chr11:65294000-65306800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:65294000-65307000	Strong transcription	Lung	lung
49	chr11:65294000-65307200	Strong transcription	Brain Cingulate Gyrus	brain
50	chr11:65294200-65294800	Strong transcription	Colon Smooth Muscle	Colon

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