Variant report

Variant	rs11621026
Chromosome Location	chr14:64389502-64389503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64319548..64321513-chr14:64388971..64391619,2	MCF-7	breast:
2	chr14:64387137..64389678-chr14:64400895..64402635,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10873172	0.81[CHB][hapmap]
rs11158521	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11623256	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12878312	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17101465	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35539333	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4899122	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4899123	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4902254	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55989826	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56028641	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56259838	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7155075	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv564904	chr14:64346190-64416898	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1793389	chr14:64346190-64457224	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11621026	C14orf39	cis	cerebellum	SCAN
rs11621026	SYNE2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
2	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
3	chr14:64365400-64393600	Weak transcription	Right Ventricle	heart
4	chr14:64374600-64399600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr14:64375200-64395000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr14:64375200-64395200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr14:64375800-64393200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:64376000-64389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr14:64376000-64389600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr14:64376000-64389600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr14:64376000-64391200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr14:64376000-64399200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr14:64376000-64399600	Weak transcription	Small Intestine	intestine
14	chr14:64376000-64399800	Weak transcription	Primary T cells from cord blood	blood
15	chr14:64376000-64416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr14:64376200-64399400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr14:64376400-64394000	Weak transcription	Lung	lung
18	chr14:64378000-64394800	Weak transcription	Fetal Heart	heart
19	chr14:64378000-64404800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr14:64378000-64416200	Weak transcription	Fetal Lung	lung
21	chr14:64378400-64416000	Weak transcription	Primary B cells from cord blood	blood
22	chr14:64378800-64390600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:64378800-64401200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:64379200-64389600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr14:64379800-64409000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr14:64381400-64395200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr14:64383600-64389800	Weak transcription	GM12878-XiMat	blood
28	chr14:64384200-64399600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr14:64385200-64391600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr14:64385600-64395600	Weak transcription	Ovary	ovary
31	chr14:64385800-64389800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr14:64386400-64390200	Weak transcription	Fetal Stomach	stomach
33	chr14:64386400-64403800	Weak transcription	Esophagus	oesophagus
34	chr14:64386400-64405600	Weak transcription	Pancreas	Pancrea
35	chr14:64386600-64390000	Weak transcription	Left Ventricle	heart
36	chr14:64386600-64403400	Weak transcription	Gastric	stomach
37	chr14:64387000-64389600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr14:64387000-64389800	Weak transcription	Fetal Kidney	kidney
39	chr14:64387000-64404200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr14:64387000-64416400	Weak transcription	Aorta	Aorta
41	chr14:64387200-64390000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr14:64387200-64390200	Weak transcription	Fetal Muscle Leg	muscle
43	chr14:64387200-64396600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:64387200-64399800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr14:64387400-64390400	Weak transcription	Fetal Brain Female	brain
46	chr14:64387400-64393200	Weak transcription	Dnd41	blood
47	chr14:64387400-64396400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr14:64387400-64399800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr14:64387600-64389600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr14:64387600-64393400	Weak transcription	Primary T cells fromperipheralblood	blood

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