Variant report

Variant	rs1787663
Chromosome Location	chr11:65294830-65294831
allele	A/C
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
ENSG00000197136	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000173327	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10896012	0.85[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs10896015	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs10896016	0.80[JPT][hapmap]
rs11227221	0.80[JPT][hapmap]
rs1143756	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1151517	0.80[JPT][hapmap]
rs1152619	0.88[TSI][hapmap]
rs1152620	0.84[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs11601767	0.80[JPT][hapmap];0.81[TSI][hapmap]
rs1194076	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs12270054	0.90[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs1346	0.89[JPT][hapmap]
rs1783541	0.90[CEU][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs3200401	0.85[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs3782091	0.80[JPT][hapmap]
rs4244811	0.80[JPT][hapmap]
rs600231	0.84[TSI][hapmap]
rs947791	0.90[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 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
19	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1787663	LINS1	trans	parietal	SCAN
rs1787663	CDK2AP2	cis	cerebellum	SCAN
rs1787663	TTC9C	cis	parietal	SCAN
rs1787663	SCGB2A1	cis	cerebellum	SCAN
rs1787663	LTBP3	cis	cerebellum	SCAN
rs1787663	TPCN2	cis	parietal	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	chr11:65293600-65295000	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr11:65293600-65297400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:65293600-65297600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:65293600-65297600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:65293600-65297800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:65293600-65299000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:65293600-65300200	Weak transcription	Psoas Muscle	Psoas
9	chr11:65293600-65305600	Weak transcription	Right Atrium	heart
10	chr11:65293600-65307600	Weak transcription	Small Intestine	intestine
11	chr11:65293800-65295400	Strong transcription	Fetal Kidney	kidney
12	chr11:65293800-65295600	Genic enhancers	Liver	Liver
13	chr11:65293800-65296000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:65293800-65296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:65293800-65297600	Weak transcription	A549	lung
16	chr11:65293800-65298000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:65293800-65302800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:65294000-65295000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr11:65294000-65295000	Strong transcription	Ovary	ovary
20	chr11:65294000-65295800	Weak transcription	Primary B cells from cord blood	blood
21	chr11:65294000-65296200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:65294000-65296400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:65294000-65296800	Strong transcription	Thymus	Thymus
24	chr11:65294000-65297000	Weak transcription	Left Ventricle	heart
25	chr11:65294000-65297200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:65294000-65297200	Weak transcription	Brain Angular Gyrus	brain
27	chr11:65294000-65298200	Weak transcription	Stomach Mucosa	stomach
28	chr11:65294000-65300200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:65294000-65300600	Strong transcription	HSMM	muscle
30	chr11:65294000-65300800	Strong transcription	Colonic Mucosa	Colon
31	chr11:65294000-65301400	Strong transcription	Esophagus	oesophagus
32	chr11:65294000-65305800	Strong transcription	Fetal Brain Female	brain
33	chr11:65294000-65305800	Strong transcription	Fetal Intestine Large	intestine
34	chr11:65294000-65306400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:65294000-65306400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr11:65294000-65306400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr11:65294000-65306600	Weak transcription	Fetal Heart	heart
38	chr11:65294000-65306800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:65294000-65307000	Strong transcription	Lung	lung
40	chr11:65294000-65307200	Strong transcription	Brain Cingulate Gyrus	brain
41	chr11:65294200-65295000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr11:65294200-65295000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:65294200-65295000	Strong transcription	HMEC	breast
44	chr11:65294200-65295000	Strong transcription	NHDF-Ad	bronchial
45	chr11:65294200-65295200	Strong transcription	Brain Anterior Caudate	brain
46	chr11:65294200-65295600	Strong transcription	Fetal Lung	lung
47	chr11:65294200-65295800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr11:65294200-65296000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:65294200-65296400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:65294200-65296400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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