Variant report

Variant	rs12883728
Chromosome Location	chr14:64330474-64330475
allele	A/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	POLR2A	chr14:64330390-64331630	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64319483..64322302-chr14:64328481..64332813,5	MCF-7	breast:
2	chr14:64319166..64320923-chr14:64328806..64331982,4	MCF-7	breast:

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

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10140978	0.82[CEU][hapmap]
rs12879641	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12880477	0.97[ASN][1000 genomes]
rs12881241	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12882972	1.00[ASN][1000 genomes]
rs12884259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889107	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12889504	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894035	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894619	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896216	0.97[ASN][1000 genomes]
rs12898127	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17101419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17101437	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17225497	0.97[ASN][1000 genomes]
rs1890908	0.82[CEU][hapmap]
rs1959033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356994	0.97[ASN][1000 genomes]
rs34252863	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34292510	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34294645	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35103832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35244884	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35353466	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35499091	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35635100	1.00[ASN][1000 genomes]
rs35672192	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35752453	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35773852	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35860218	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57010514	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71416311	1.00[ASN][1000 genomes]
rs71416313	1.00[ASN][1000 genomes]
rs71416318	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71437513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003797	1.00[ASN][1000 genomes]
rs9707777	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64321200-64333800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:64321200-64334600	Weak transcription	Pancreas	Pancrea
3	chr14:64321200-64340600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:64321400-64330600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr14:64321400-64331200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:64321400-64350200	Weak transcription	Fetal Stomach	stomach
7	chr14:64322400-64334400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr14:64322600-64331200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:64322600-64331200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr14:64322800-64330600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr14:64322800-64330800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr14:64322800-64340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:64322800-64340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:64323000-64332800	Weak transcription	Fetal Intestine Small	intestine
15	chr14:64323000-64333000	Weak transcription	Ovary	ovary
16	chr14:64323200-64331200	Weak transcription	Right Atrium	heart
17	chr14:64323200-64334400	Weak transcription	Aorta	Aorta
18	chr14:64323200-64340200	Weak transcription	Left Ventricle	heart
19	chr14:64323200-64340400	Weak transcription	Spleen	Spleen
20	chr14:64324200-64330800	Weak transcription	Hela-S3	cervix
21	chr14:64324400-64330800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:64324400-64331200	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr14:64324600-64331000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr14:64324600-64331200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:64324600-64341400	Weak transcription	HSMM	muscle
26	chr14:64325800-64331000	Enhancers	Placenta	Placenta
27	chr14:64326600-64330800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr14:64326800-64331600	Enhancers	Stomach Mucosa	stomach
29	chr14:64327000-64330600	Enhancers	Dnd41	blood
30	chr14:64327000-64331400	Weak transcription	Thymus	Thymus
31	chr14:64327200-64331200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr14:64327200-64332000	Weak transcription	Fetal Brain Female	brain
33	chr14:64327200-64340600	Weak transcription	Right Ventricle	heart
34	chr14:64327400-64330800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr14:64327400-64330800	Weak transcription	Fetal Intestine Large	intestine
36	chr14:64327400-64331000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr14:64327400-64331000	Weak transcription	Fetal Heart	heart
38	chr14:64327400-64333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr14:64327600-64360000	Weak transcription	Gastric	stomach
41	chr14:64327800-64334400	Weak transcription	Lung	lung
42	chr14:64327800-64342200	Weak transcription	Esophagus	oesophagus
43	chr14:64328400-64330600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr14:64328400-64335000	Weak transcription	Psoas Muscle	Psoas
45	chr14:64328600-64331400	Flanking Active TSS	GM12878-XiMat	blood
46	chr14:64329000-64330800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr14:64329000-64331200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr14:64329000-64331600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:64329200-64330600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr14:64329200-64330600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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