Variant report

Variant	rs6573535
Chromosome Location	chr14:64330696-64330697
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	CBX3	chr14:64330605-64331505	HCT-116	colon:	n/a	n/a
2	POLR2A	chr14:64330390-64331630	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr14:64330695-64331458	MCF10A-Er-Src	breast:	n/a	chr14:64331205-64331214 chr14:64330854-64330862
4	SP1	chr14:64330531-64331488	HCT-116	colon:	n/a	n/a
5	MAX	chr14:64330615-64331475	HCT-116	colon:	n/a	n/a
6	FOSL1	chr14:64330604-64331557	HCT-116	colon:	n/a	chr14:64331206-64331213 chr14:64331204-64331213 chr14:64331203-64331215 chr14:64331204-64331214 chr14:64331205-64331214 chr14:64331501-64331512
7	JUND	chr14:64330647-64331564	HCT-116	colon:	n/a	chr14:64331206-64331213 chr14:64331204-64331213 chr14:64331203-64331215 chr14:64331203-64331214 chr14:64331204-64331214 chr14:64331205-64331214 chr14:64331501-64331512
8	CEBPB	chr14:64330628-64331467	HCT-116	colon:	n/a	n/a
9	SP1	chr14:64330595-64331559	HCT-116	colon:	n/a	n/a
10	CEBPB	chr14:64330517-64331645	HCT-116	colon:	n/a	n/a
11	TCF12	chr14:64330663-64331464	A549	lung:	n/a	n/a
12	CBX3	chr14:64330522-64331523	HCT-116	colon:	n/a	n/a
13	MAX	chr14:64330659-64331477	HCT-116	colon:	n/a	n/a
14	JUND	chr14:64330652-64331523	HCT-116	colon:	n/a	chr14:64331206-64331213 chr14:64331204-64331213 chr14:64331203-64331215 chr14:64331203-64331214 chr14:64331204-64331214 chr14:64331205-64331214 chr14:64331501-64331512
15	STAT1	chr14:64330684-64331642	Hela-S3	cervix:	n/a	chr14:64331205-64331214 chr14:64331596-64331604 chr14:64330854-64330862

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: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1000904	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10873171	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11158515	0.87[CHB][hapmap]
rs11158516	0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs11158518	0.87[CHB][hapmap]
rs11626911	0.83[CHB][hapmap]
rs11628650	0.87[CHB][hapmap]
rs12431956	0.87[CHB][hapmap]
rs12435958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12436656	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12587452	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12893838	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1959034	0.89[YRI][hapmap]
rs2151763	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2210650	0.81[AFR][1000 genomes]
rs2357001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34486661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35234298	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36050513	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902249	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902251	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902252	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4902253	0.87[CHB][hapmap]
rs55925976	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61985747	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573532	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573533	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573536	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7144370	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7145302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7145810	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7146821	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs7149609	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7150540	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7153723	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7158960	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7161586	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8004989	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8009846	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8010094	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8010312	0.83[CHB][hapmap]
rs8013611	0.96[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs8017009	0.87[CHB][hapmap]
rs945031	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs951250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs954730	0.84[YRI][hapmap]
rs998241	0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs998242	0.87[CHB][hapmap];0.80[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:78 , 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	chr14:64321400-64331200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:64321400-64350200	Weak transcription	Fetal Stomach	stomach
6	chr14:64322400-64334400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:64322600-64331200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr14:64322600-64331200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr14:64322800-64330800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr14:64322800-64340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:64322800-64340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:64323000-64332800	Weak transcription	Fetal Intestine Small	intestine
13	chr14:64323000-64333000	Weak transcription	Ovary	ovary
14	chr14:64323200-64331200	Weak transcription	Right Atrium	heart
15	chr14:64323200-64334400	Weak transcription	Aorta	Aorta
16	chr14:64323200-64340200	Weak transcription	Left Ventricle	heart
17	chr14:64323200-64340400	Weak transcription	Spleen	Spleen
18	chr14:64324200-64330800	Weak transcription	Hela-S3	cervix
19	chr14:64324400-64330800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr14:64324400-64331200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr14:64324600-64331000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr14:64324600-64331200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr14:64324600-64341400	Weak transcription	HSMM	muscle
24	chr14:64325800-64331000	Enhancers	Placenta	Placenta
25	chr14:64326600-64330800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr14:64326800-64331600	Enhancers	Stomach Mucosa	stomach
27	chr14:64327000-64331400	Weak transcription	Thymus	Thymus
28	chr14:64327200-64331200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr14:64327200-64332000	Weak transcription	Fetal Brain Female	brain
30	chr14:64327200-64340600	Weak transcription	Right Ventricle	heart
31	chr14:64327400-64330800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr14:64327400-64330800	Weak transcription	Fetal Intestine Large	intestine
33	chr14:64327400-64331000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr14:64327400-64331000	Weak transcription	Fetal Heart	heart
35	chr14:64327400-64333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr14:64327600-64360000	Weak transcription	Gastric	stomach
38	chr14:64327800-64334400	Weak transcription	Lung	lung
39	chr14:64327800-64342200	Weak transcription	Esophagus	oesophagus
40	chr14:64328400-64335000	Weak transcription	Psoas Muscle	Psoas
41	chr14:64328600-64331400	Flanking Active TSS	GM12878-XiMat	blood
42	chr14:64329000-64330800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr14:64329000-64331200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr14:64329000-64331600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr14:64329200-64334400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr14:64329600-64330800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr14:64329600-64331400	Enhancers	Small Intestine	intestine
48	chr14:64329800-64330800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr14:64329800-64330800	Weak transcription	HSMMtube	muscle
50	chr14:64329800-64331000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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