Variant report

Variant	rs4902253
Chromosome Location	chr14:64372090-64372091
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	KAP1	chr14:64370981-64372134	HEK293	kidney:	n/a	n/a
2	SETDB1	chr14:64371116-64372181	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
SYNE2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11158515	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11158518	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626911	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628650	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12161903	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12431956	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12432760	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12435958	0.87[CHB][hapmap]
rs12586461	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12590842	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12893838	0.80[ASN][1000 genomes]
rs17750888	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17750906	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1958413	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2357001	0.87[CHB][hapmap];0.92[CHD][hapmap]
rs4899121	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56376318	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60305436	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61985726	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61985748	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6573535	0.87[CHB][hapmap]
rs66460676	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66764453	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67011590	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67106029	0.88[ASN][1000 genomes]
rs67975797	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7140278	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7143794	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7145302	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs7145736	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7146469	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7149405	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73276854	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8008800	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8010312	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs8010385	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8013611	0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8016321	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8017009	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs951249	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs951250	0.87[CHB][hapmap]
rs998242	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4902253	SYNE2	cis	cerebellum	SCAN
rs4902253	FLJ43390	cis	cerebellum	SCAN
rs4902253	C14orf39	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
2	chr14:64358200-64375800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:64358200-64377600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:64358800-64377600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr14:64360600-64382200	Weak transcription	Psoas Muscle	Psoas
6	chr14:64360800-64374200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr14:64360800-64377800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr14:64361200-64373600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:64363400-64374400	Weak transcription	Fetal Intestine Small	intestine
10	chr14:64363400-64375200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:64363400-64375400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:64363800-64375400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr14:64364400-64385200	Weak transcription	Pancreas	Pancrea
14	chr14:64364600-64375400	Weak transcription	Aorta	Aorta
15	chr14:64364600-64387800	Weak transcription	HMEC	breast
16	chr14:64364800-64375400	Weak transcription	Hela-S3	cervix
17	chr14:64365000-64374200	Weak transcription	Brain Germinal Matrix	brain
18	chr14:64365000-64375000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:64365000-64375000	Weak transcription	Fetal Kidney	kidney
20	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
21	chr14:64365200-64375800	Weak transcription	Fetal Stomach	stomach
22	chr14:64365200-64386200	Weak transcription	Gastric	stomach
23	chr14:64365400-64376600	Weak transcription	Placenta	Placenta
24	chr14:64365400-64379800	Weak transcription	Fetal Thymus	thymus
25	chr14:64365400-64393600	Weak transcription	Right Ventricle	heart
26	chr14:64365600-64375400	Weak transcription	Stomach Mucosa	stomach
27	chr14:64367400-64375200	Weak transcription	Right Atrium	heart
28	chr14:64367400-64375400	Weak transcription	Left Ventricle	heart
29	chr14:64367400-64378000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr14:64367600-64374000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr14:64367800-64373600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr14:64367800-64377400	Weak transcription	Primary B cells from cord blood	blood
33	chr14:64368600-64375400	Weak transcription	Dnd41	blood
34	chr14:64368600-64375400	Weak transcription	Osteobl	bone
35	chr14:64368800-64374200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr14:64369000-64373200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr14:64369400-64375400	Weak transcription	Adipose Nuclei	Adipose
38	chr14:64369600-64374200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr14:64369600-64375000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr14:64369600-64375200	Weak transcription	Ovary	ovary
41	chr14:64369600-64375400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr14:64369600-64377600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr14:64369800-64374400	Weak transcription	Small Intestine	intestine
44	chr14:64369800-64374800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr14:64369800-64376200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr14:64369800-64376400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr14:64369800-64386200	Weak transcription	Esophagus	oesophagus
48	chr14:64370000-64373000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr14:64370000-64373400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr14:64370800-64375400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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