Variant report

Variant	rs3783653
Chromosome Location	chr14:55855007-55855008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55831903..55834657-chr14:55852806..55855439,2	MCF-7	breast:

Extended variants
information (count: 7 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17742886	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9323283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS 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 target site	20 gene(s)	inside rSNPs	diseases
3	nsv901959	chr14:55853724-55916225	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
4	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3783653	SCLY	trans	cerebellum	SCAN
rs3783653	ATG14	cis	parietal	SCAN
rs3783653	FBXO34	cis	cerebellum	SCAN
rs3783653	EXOC5	cis	cerebellum	SCAN
rs3783653	CNIH	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55808800-55865200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:55818200-55877600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:55818400-55858800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:55819400-55855200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:55821400-55865200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:55831000-55859400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr14:55831800-55858000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr14:55832400-55857800	Strong transcription	Liver	Liver
9	chr14:55836800-55877800	Weak transcription	Esophagus	oesophagus
10	chr14:55839400-55859200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr14:55839600-55858600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr14:55840200-55858800	Strong transcription	Primary B cells from cord blood	blood
13	chr14:55840400-55856600	Strong transcription	Fetal Intestine Large	intestine
14	chr14:55840400-55856800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:55841000-55859000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr14:55842000-55856200	Strong transcription	Fetal Muscle Leg	muscle
17	chr14:55842200-55856400	Strong transcription	Placenta	Placenta
18	chr14:55842400-55855400	Strong transcription	Fetal Stomach	stomach
19	chr14:55845000-55855200	Strong transcription	Fetal Intestine Small	intestine
20	chr14:55847200-55855400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr14:55847200-55856800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr14:55848600-55856200	Strong transcription	HepG2	liver
23	chr14:55848600-55876600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr14:55848800-55855800	Weak transcription	Brain Angular Gyrus	brain
25	chr14:55848800-55861000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr14:55848800-55861200	Weak transcription	Small Intestine	intestine
27	chr14:55848800-55861800	Weak transcription	HUVEC	blood vessel
28	chr14:55848800-55864600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr14:55848800-55865000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr14:55849000-55856000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr14:55849200-55876600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr14:55849200-55878000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr14:55849600-55855800	Weak transcription	Fetal Lung	lung
34	chr14:55849800-55865200	Weak transcription	A549	lung
35	chr14:55850000-55868400	Weak transcription	Right Ventricle	heart
36	chr14:55850400-55856200	Strong transcription	Ovary	ovary
37	chr14:55850400-55856600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr14:55850400-55856600	Strong transcription	Fetal Brain Female	brain
39	chr14:55850400-55857000	Strong transcription	Primary T cells from cord blood	blood
40	chr14:55850600-55856800	Strong transcription	Fetal Thymus	thymus
41	chr14:55850600-55856800	Strong transcription	Dnd41	blood
42	chr14:55850600-55858000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr14:55850800-55856600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr14:55850800-55861400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr14:55850800-55865400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:55850800-55865400	Weak transcription	Aorta	Aorta
47	chr14:55851000-55855800	Weak transcription	Fetal Heart	heart
48	chr14:55851000-55871000	Weak transcription	Pancreas	Pancrea
49	chr14:55851600-55859000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr14:55851800-55855400	Weak transcription	Psoas Muscle	Psoas

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