Variant report

Variant	rs1255994
Chromosome Location	chr14:64664494-64664495
allele	G/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	REST	chr14:64662665-64665717	H1-neurons	neurons:	n/a	chr14:64663684-64663704 chr14:64663869-64663878 chr14:64663684-64663704 chr14:64663684-64663704 chr14:64663726-64663739
2	IRF3	chr14:64664426-64664528	GM12878	blood:	n/a	n/a
3	MXI1	chr14:64663169-64664777	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:64662559..64666637-chr14:64681435..64684914,4	MCF-7	breast:
2	chr14:64660992..64662814-chr14:64664224..64665884,2	MCF-7	breast:
3	chr14:64662914..64664547-chr14:64673887..64676659,2	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1152596	1.00[MEX][hapmap]
rs1152597	0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1152598	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152600	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255980	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255981	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1255982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1255983	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1255993	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1255996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256034	1.00[MEX][hapmap]
rs1256104	1.00[MEX][hapmap]
rs1266926	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1271028	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs944461	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv902021	chr14:64647646-64715794	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64600600-64667400	Weak transcription	Stomach Mucosa	stomach
2	chr14:64650800-64671800	Strong transcription	Liver	Liver
3	chr14:64652800-64666200	Strong transcription	Dnd41	blood
4	chr14:64658200-64667000	Weak transcription	Esophagus	oesophagus
5	chr14:64660600-64665200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr14:64660800-64682600	Weak transcription	Hela-S3	cervix
7	chr14:64661600-64667000	Weak transcription	HepG2	liver
8	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr14:64661800-64675400	Weak transcription	NHEK	skin
11	chr14:64661800-64675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr14:64662400-64675200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr14:64662600-64665400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr14:64662800-64665600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr14:64662800-64667400	Weak transcription	Lung	lung
16	chr14:64662800-64674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr14:64663200-64665200	Active TSS	Brain Angular Gyrus	brain
18	chr14:64663200-64665400	Active TSS	Brain Anterior Caudate	brain
19	chr14:64663200-64667400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr14:64663400-64664600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:64663400-64664600	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr14:64663400-64664600	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr14:64663400-64664600	Active TSS	Brain Germinal Matrix	brain
24	chr14:64663400-64664600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr14:64663400-64664600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr14:64663400-64664600	Active TSS	Brain Substantia Nigra	brain
27	chr14:64663400-64664800	Active TSS	Brain Cingulate Gyrus	brain
28	chr14:64663400-64664800	Active TSS	Right Atrium	heart
29	chr14:64663600-64664600	Active TSS	Brain Hippocampus Middle	brain
30	chr14:64663800-64665400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr14:64663800-64668600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr14:64664000-64664600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr14:64664000-64664600	Active TSS	Primary T cells from cord blood	blood
34	chr14:64664000-64664600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr14:64664000-64664600	Flanking Active TSS	Fetal Brain Male	brain
36	chr14:64664000-64664600	Flanking Active TSS	Fetal Brain Female	brain
37	chr14:64664000-64665000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr14:64664000-64665000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr14:64664000-64665200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr14:64664000-64665800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr14:64664000-64665800	Weak transcription	Gastric	stomach
42	chr14:64664000-64667000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr14:64664000-64667000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr14:64664000-64667200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr14:64664000-64667400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr14:64664000-64668000	Weak transcription	Spleen	Spleen
47	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
48	chr14:64664200-64664600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr14:64664200-64664600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr14:64664200-64664800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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