Variant report

Variant	rs11849394
Chromosome Location	chr14:64583810-64583811
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	E2F4	chr14:64583629-64583816	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr14:64578683-64586884	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr14:64578631-64587093	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64517201..64519341-chr14:64582124..64585042,2	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10047814	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10047815	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs10047901	0.94[ASN][1000 genomes]
rs10136099	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10136662	0.87[ASW][hapmap];0.85[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10137370	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10137426	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10137665	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10142318	0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10142480	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10151446	1.00[ASN][1000 genomes]
rs11158531	0.90[ASN][1000 genomes]
rs11158532	0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12147438	0.88[ASN][1000 genomes]
rs12587140	0.87[ASN][1000 genomes]
rs12587924	0.95[ASN][1000 genomes]
rs12590062	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2184288	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34994562	0.90[ASN][1000 genomes]
rs45472593	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57018718	0.94[ASN][1000 genomes]
rs57034528	0.91[ASN][1000 genomes]
rs7140578	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7158393	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7159213	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7160091	0.85[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7161361	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8003196	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8021831	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8022222	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023139	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9323446	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[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	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11849394	SNAPC1	cis	parietal	SCAN
rs11849394	FLJ43390	cis	parietal	SCAN
rs11849394	PPM1A	cis	parietal	SCAN
rs11849394	FNTB	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64466600-64593200	Weak transcription	Colon Smooth Muscle	Colon
2	chr14:64519400-64592000	Weak transcription	Fetal Brain Male	brain
3	chr14:64544000-64616200	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr14:64548400-64590800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr14:64562800-64596200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:64565800-64588600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr14:64567200-64616200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:64567400-64647200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:64567800-64584800	Weak transcription	Fetal Heart	heart
10	chr14:64568800-64590000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:64569000-64587800	Weak transcription	Small Intestine	intestine
12	chr14:64570800-64587600	Weak transcription	Primary B cells from cord blood	blood
13	chr14:64572800-64586000	Weak transcription	Fetal Lung	lung
14	chr14:64574600-64584200	Weak transcription	HUVEC	blood vessel
15	chr14:64574600-64591800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:64574800-64586000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr14:64574800-64586200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr14:64575000-64584600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr14:64575800-64585600	Weak transcription	Ovary	ovary
20	chr14:64577800-64616200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr14:64578200-64649000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr14:64578600-64649000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:64579600-64585000	Strong transcription	Fetal Stomach	stomach
24	chr14:64579600-64611000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr14:64580200-64586200	Weak transcription	Aorta	Aorta
26	chr14:64580400-64588400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr14:64580600-64585600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr14:64580600-64585800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr14:64580600-64586400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr14:64580600-64589800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr14:64580600-64600200	Weak transcription	Stomach Mucosa	stomach
32	chr14:64581000-64592200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr14:64581200-64584200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr14:64581200-64584400	Weak transcription	HSMM	muscle
35	chr14:64581200-64587800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr14:64581200-64588800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:64581200-64593200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr14:64581400-64584400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr14:64581400-64584400	Weak transcription	HSMMtube	muscle
40	chr14:64581400-64588400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr14:64581400-64592600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr14:64581400-64613400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr14:64581800-64587800	Weak transcription	Fetal Kidney	kidney
44	chr14:64581800-64589000	Weak transcription	Esophagus	oesophagus
45	chr14:64581800-64650400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr14:64582000-64589000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr14:64582000-64589000	Weak transcription	Right Ventricle	heart
48	chr14:64582000-64589200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr14:64582000-64589200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr14:64582200-64584400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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