Variant report

Variant	rs11622858
Chromosome Location	chr14:64526751-64526752
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	POLR2A	chr14:64526135-64527725	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr14:64526707-64526833	GM12878	blood:	n/a	n/a

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

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

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10135588	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10140978	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10146667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11844088	0.81[ASN][1000 genomes]
rs11844628	0.81[ASN][1000 genomes]
rs1255948	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255950	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255951	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255952	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255955	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255960	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255961	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255964	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255965	0.83[ASN][1000 genomes]
rs1255968	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12586503	0.81[ASN][1000 genomes]
rs1262241	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12894671	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1890907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1890908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2153477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2153478	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2153481	0.85[ASN][1000 genomes]
rs2781377	0.83[AMR][1000 genomes]
rs2781378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3866737	0.81[ASN][1000 genomes]
rs4027405	0.81[ASN][1000 genomes]
rs4899131	0.81[ASN][1000 genomes]
rs6573542	0.81[ASN][1000 genomes]
rs6573544	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7146859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7147157	0.81[ASN][1000 genomes]
rs7150982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7153376	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7157993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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	chr14:64468800-64527200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:64475200-64527200	Weak transcription	Fetal Heart	heart
4	chr14:64481400-64574000	Weak transcription	Stomach Mucosa	stomach
5	chr14:64489400-64568600	Weak transcription	Small Intestine	intestine
6	chr14:64491200-64565200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr14:64492200-64547400	Weak transcription	Colonic Mucosa	Colon
8	chr14:64499000-64538800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:64510600-64527200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:64511200-64527000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr14:64512400-64527600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr14:64514600-64527200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr14:64515000-64527600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:64515600-64526800	Weak transcription	Hela-S3	cervix
15	chr14:64516600-64541400	Weak transcription	HSMM	muscle
16	chr14:64518000-64527400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:64519000-64527000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr14:64519000-64527200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr14:64519000-64528000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:64519000-64541000	Weak transcription	HUVEC	blood vessel
21	chr14:64519200-64533200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr14:64519400-64526800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr14:64519400-64527000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:64519400-64529600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr14:64519400-64592000	Weak transcription	Fetal Brain Male	brain
26	chr14:64519600-64527000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr14:64519600-64529600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr14:64519600-64539000	Weak transcription	Right Ventricle	heart
29	chr14:64519600-64545200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr14:64519800-64527000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr14:64519800-64532000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr14:64519800-64534600	Weak transcription	Fetal Lung	lung
33	chr14:64520000-64527000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr14:64520000-64527200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:64520200-64527000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr14:64520400-64537400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr14:64520400-64539000	Weak transcription	Liver	Liver
38	chr14:64520600-64526800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr14:64520600-64527400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr14:64520600-64530000	Weak transcription	GM12878-XiMat	blood
41	chr14:64521000-64529800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr14:64521000-64540800	Weak transcription	Psoas Muscle	Psoas
43	chr14:64522600-64528000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr14:64523000-64532200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr14:64523200-64529600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr14:64524200-64532000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr14:64524400-64527000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr14:64525200-64527400	Strong transcription	Fetal Muscle Leg	muscle
49	chr14:64525400-64527400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr14:64525400-64535400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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