Variant report

Variant	rs3759053
Chromosome Location	chr11:64323080-64323081
allele	A/G
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	chr11:64322978-64323234	HepG2	liver:	n/a	n/a
2	RAD21	chr11:64323019-64323086	HepG2	liver:	n/a	n/a
3	MAX	chr11:64322711-64323400	A549	lung:	n/a	n/a
4	FOXA2	chr11:64322902-64323143	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:64322999-64323319	HepG2	liver:	n/a	n/a
6	MYBL2	chr11:64322873-64323312	HepG2	liver:	n/a	n/a
7	ARID3A	chr11:64322882-64323208	HepG2	liver:	n/a	n/a
8	MAFF	chr11:64323014-64323236	HepG2	liver:	n/a	n/a
9	JUND	chr11:64322913-64323299	HepG2	liver:	n/a	n/a
10	HEY1	chr11:64322958-64323513	HepG2	liver:	n/a	n/a
11	CTCF	chr11:64323000-64323150	HCPEpiC	choroid plexus:	n/a	n/a
12	CEBPB	chr11:64322908-64323108	A549	lung:	n/a	n/a
13	MAZ	chr11:64323033-64323282	HepG2	liver:	n/a	n/a
14	JUN	chr11:64322547-64323823	K562	blood:	n/a	n/a
15	CEBPB	chr11:64322854-64323194	HepG2	liver:	n/a	n/a
16	CEBPB	chr11:64322947-64323104	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SLC22A11	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11231808	0.81[ASN][1000 genomes]
rs11231815	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11231822	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362644	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12417589	0.81[ASN][1000 genomes]
rs12808503	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17300741	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17300895	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17372915	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2078267	0.89[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2277312	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34812986	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3782099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930195	1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4930426	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57827982	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6591859	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7102027	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7123852	0.81[ASN][1000 genomes]
rs7124676	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71456318	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7929308	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940321	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035485	chr11:64228847-64354869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897692	chr11:64305452-64386526	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
3	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3759053	TBC1D10C	cis	cerebellum	SCAN
rs3759053	MARK2	cis	parietal	SCAN
rs3759053	RAB3IL1	cis	parietal	SCAN
rs3759053	RTN3	cis	parietal	SCAN
rs3759053	PYGM	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64320600-64323600	Enhancers	Fetal Lung	lung
2	chr11:64320600-64324400	Enhancers	Spleen	Spleen
3	chr11:64320800-64323400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:64320800-64323400	Enhancers	Placenta	Placenta
5	chr11:64320800-64323600	Enhancers	Fetal Stomach	stomach
6	chr11:64320800-64323600	Enhancers	Ovary	ovary
7	chr11:64320800-64324600	Enhancers	Fetal Muscle Leg	muscle
8	chr11:64320800-64324800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:64320800-64326000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:64321000-64323200	Enhancers	Fetal Muscle Trunk	muscle
11	chr11:64321200-64323200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr11:64321200-64323200	Enhancers	Primary B cells from cord blood	blood
13	chr11:64321200-64323200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:64321200-64323200	Enhancers	NHDF-Ad	bronchial
15	chr11:64321200-64323400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:64321200-64323400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:64321200-64323400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:64321200-64323400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:64321200-64323400	Enhancers	Adipose Nuclei	Adipose
20	chr11:64321200-64323400	Enhancers	Brain Cingulate Gyrus	brain
21	chr11:64321200-64323400	Enhancers	Brain Substantia Nigra	brain
22	chr11:64321200-64323400	Enhancers	Colon Smooth Muscle	Colon
23	chr11:64321200-64323400	Enhancers	Rectal Smooth Muscle	rectum
24	chr11:64321200-64323400	Enhancers	Osteobl	bone
25	chr11:64321200-64323600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:64321200-64323600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr11:64321200-64323600	Enhancers	Colonic Mucosa	Colon
28	chr11:64321200-64323600	Enhancers	HSMM	muscle
29	chr11:64321200-64323600	Enhancers	HSMMtube	muscle
30	chr11:64321200-64323600	Enhancers	NH-A	brain
31	chr11:64321200-64324000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr11:64321200-64324200	Enhancers	Fetal Thymus	thymus
33	chr11:64321200-64324400	Enhancers	Fetal Intestine Small	intestine
34	chr11:64321200-64325000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr11:64321200-64325200	Enhancers	Fetal Intestine Large	intestine
36	chr11:64321400-64323200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:64321400-64323400	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr11:64321400-64323600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:64321400-64324200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:64321600-64323200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr11:64321600-64323200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr11:64321600-64324600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:64321600-64324800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr11:64321600-64325000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:64321800-64323200	Weak transcription	Right Ventricle	heart
46	chr11:64321800-64323400	Enhancers	Primary hematopoietic stem cells	blood
47	chr11:64321800-64323600	Enhancers	Placenta Amnion	Placenta Amnion
48	chr11:64321800-64324600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:64321800-64325800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr11:64321800-64325800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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