Variant report

Variant	rs10140978
Chromosome Location	chr14:64528071-64528072
allele	A/G
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	YY1	chr14:64527388-64528072	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64526121..64529076-chr14:64529441..64531025,2	MCF-7	breast:
2	chr14:64526854..64528151-chr14:64761355..64762258,4	MCF-7	breast:

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

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10135588	0.88[EUR][1000 genomes]
rs10146667	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10151127	0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11622858	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255948	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255950	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255951	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255952	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255955	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255959	0.82[CHB][hapmap]
rs1255960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255965	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1255967	0.85[GIH][hapmap]
rs1255968	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255973	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1262240	0.83[GIH][hapmap]
rs1262241	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883728	0.82[CEU][hapmap]
rs12887573	0.82[CEU][hapmap]
rs12894671	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17101419	0.82[CEU][hapmap]
rs1890907	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1890908	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1959033	0.82[CEU][hapmap]
rs2153477	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2153478	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2781377	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs2781378	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28572628	0.84[ASN][1000 genomes]
rs3829767	0.85[GIH][hapmap]
rs4027402	0.81[JPT][hapmap]
rs4027404	0.81[JPT][hapmap]
rs4027405	0.91[CHD][hapmap]
rs4275767	0.91[ASN][1000 genomes]
rs4462521	0.84[ASN][1000 genomes]
rs6573544	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146859	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7150982	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7153376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7157594	0.84[ASN][1000 genomes]
rs7157993	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8010699	0.85[GIH][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	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	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
3	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
4	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

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64466600-64593200	Weak transcription	Colon Smooth Muscle	Colon
2	chr14:64481400-64574000	Weak transcription	Stomach Mucosa	stomach
3	chr14:64489400-64568600	Weak transcription	Small Intestine	intestine
4	chr14:64491200-64565200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:64492200-64547400	Weak transcription	Colonic Mucosa	Colon
6	chr14:64499000-64538800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr14:64516600-64541400	Weak transcription	HSMM	muscle
8	chr14:64519000-64541000	Weak transcription	HUVEC	blood vessel
9	chr14:64519200-64533200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr14:64519400-64529600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr14:64519400-64592000	Weak transcription	Fetal Brain Male	brain
12	chr14:64519600-64529600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr14:64519600-64539000	Weak transcription	Right Ventricle	heart
14	chr14:64519600-64545200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr14:64519800-64532000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr14:64519800-64534600	Weak transcription	Fetal Lung	lung
17	chr14:64520400-64537400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr14:64520400-64539000	Weak transcription	Liver	Liver
19	chr14:64520600-64530000	Weak transcription	GM12878-XiMat	blood
20	chr14:64521000-64529800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr14:64521000-64540800	Weak transcription	Psoas Muscle	Psoas
22	chr14:64523000-64532200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr14:64523200-64529600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr14:64524200-64532000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:64525400-64535400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr14:64525400-64566600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr14:64526000-64529800	Enhancers	HMEC	breast
28	chr14:64526000-64552200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr14:64526600-64529600	Weak transcription	Lung	lung
30	chr14:64526600-64529800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr14:64526600-64536000	Weak transcription	Fetal Brain Female	brain
32	chr14:64526800-64529800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr14:64526800-64534000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr14:64526800-64539000	Weak transcription	Fetal Thymus	thymus
35	chr14:64526800-64540400	Weak transcription	Fetal Kidney	kidney
36	chr14:64526800-64577000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr14:64527000-64528400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr14:64527000-64528400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr14:64527000-64528600	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr14:64527000-64528600	Flanking Active TSS	NHEK	skin
41	chr14:64527000-64529200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr14:64527000-64529400	Weak transcription	Adipose Nuclei	Adipose
43	chr14:64527000-64530000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr14:64527000-64532200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr14:64527000-64539600	Weak transcription	Ovary	ovary
46	chr14:64527000-64540200	Weak transcription	Primary B cells from cord blood	blood
47	chr14:64527000-64540800	Weak transcription	Spleen	Spleen
48	chr14:64527000-64547200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr14:64527200-64528200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr14:64527200-64529600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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