Variant report

Variant	rs4808852
Chromosome Location	chr19:18844364-18844365
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	FOXA1	chr19:18844137-18844502	HepG2	liver:	n/a	n/a
2	FOXA1	chr19:18844149-18844523	HepG2	liver:	n/a	n/a
3	EP300	chr19:18843954-18844420	SK-N-SH_RA	brain:	n/a	n/a
4	MAZ	chr19:18843850-18844717	IMR90	lung:	n/a	chr19:18844380-18844391 chr19:18844381-18844391 chr19:18844382-18844389
5	FOXA2	chr19:18844173-18844496	HepG2	liver:	n/a	n/a
6	EP300	chr19:18843597-18845272	SK-N-SH	brain:	n/a	chr19:18844438-18844448
7	EP300	chr19:18843961-18844434	SK-N-SH_RA	brain:	n/a	n/a
8	RAD21	chr19:18844156-18844537	IMR90	lung:	n/a	n/a
9	MXI1	chr19:18843813-18844802	IMR90	lung:	n/a	chr19:18844382-18844391
10	GATA2	chr19:18844047-18844490	SH-SY5Y	brain:	n/a	chr19:18844260-18844271
11	REST	chr19:18844005-18844491	SK-N-SH	brain:	n/a	n/a
12	USF1	chr19:18844193-18844486	SK-N-SH_RA	brain:	n/a	n/a
13	RCOR1	chr19:18843643-18844794	IMR90	lung:	n/a	n/a
14	FOXA1	chr19:18844049-18844565	HepG2	liver:	n/a	n/a
15	CTCF	chr19:18844320-18844470	HCPEpiC	choroid plexus:	n/a	n/a
16	MXI1	chr19:18843724-18844736	SK-N-SH	brain:	n/a	chr19:18844382-18844391

Variant related genes	Relation type
CRTC1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12984991	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17757406	1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2075017	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240014	0.82[TSI][hapmap]
rs2240887	0.83[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4808154	0.98[ASN][1000 genomes]
rs4808851	0.97[ASN][1000 genomes]
rs4808853	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56182405	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56210931	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57962499	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58406187	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61447117	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510997	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6510998	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6510999	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511000	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511001	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71332136	0.96[ASN][1000 genomes]
rs71332137	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs71332138	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7251560	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251710	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252217	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256502	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257846	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs7258259	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73537985	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73537994	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73537995	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4808852	CRTC1	cis	cerebellum	SCAN
rs4808852	DDA1	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18820400-18847200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr19:18820600-18846600	Weak transcription	Esophagus	oesophagus
3	chr19:18821200-18860600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr19:18821200-18861000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr19:18821200-18864800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr19:18824200-18846600	Weak transcription	Pancreas	Pancrea
7	chr19:18824600-18847800	Weak transcription	Liver	Liver
8	chr19:18825000-18845600	Weak transcription	Primary B cells from cord blood	blood
9	chr19:18827000-18846200	Weak transcription	Thymus	Thymus
10	chr19:18827600-18860600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:18828200-18845600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:18828800-18850400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:18829200-18860000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr19:18829200-18861400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr19:18830400-18845600	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:18830400-18845800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:18830800-18845800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr19:18833800-18853400	Weak transcription	Primary T cells from cord blood	blood
19	chr19:18833800-18860400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:18833800-18860800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:18834600-18845800	Weak transcription	Brain Anterior Caudate	brain
22	chr19:18835000-18860600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr19:18835200-18853200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:18836800-18845200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:18841000-18844800	Genic enhancers	Fetal Intestine Small	intestine
26	chr19:18841000-18845600	Enhancers	Fetal Intestine Large	intestine
27	chr19:18841200-18845000	Enhancers	HepG2	liver
28	chr19:18841200-18852000	Weak transcription	Small Intestine	intestine
29	chr19:18841600-18845800	Weak transcription	Spleen	Spleen
30	chr19:18842000-18848400	Enhancers	Fetal Muscle Leg	muscle
31	chr19:18842200-18853400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:18842600-18845800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr19:18842600-18851000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:18842600-18853400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:18842800-18845400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:18842800-18845600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:18842800-18846400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:18842800-18856600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:18842800-18861000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr19:18843000-18844400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:18843000-18845200	Enhancers	Fetal Muscle Trunk	muscle
42	chr19:18843000-18845400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:18843000-18860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:18843400-18844400	Flanking Active TSS	Fetal Heart	heart
45	chr19:18843400-18844600	Weak transcription	K562	blood
46	chr19:18843400-18845400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:18843600-18844400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr19:18843600-18844400	Enhancers	Stomach Mucosa	stomach
49	chr19:18843600-18844800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:18843600-18844800	Enhancers	Fetal Lung	lung

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