Variant report

Variant	rs10498512
Chromosome Location	chr14:64474121-64474122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10149728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873172	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs11623650	0.88[EUR][1000 genomes]
rs12147217	0.81[CHB][hapmap]
rs1255856	0.87[EUR][1000 genomes]
rs1255867	0.95[EUR][1000 genomes]
rs1255869	0.95[EUR][1000 genomes]
rs1255872	0.95[EUR][1000 genomes]
rs1255873	0.95[EUR][1000 genomes]
rs1255874	0.95[EUR][1000 genomes]
rs1255875	0.95[EUR][1000 genomes]
rs1255876	0.95[EUR][1000 genomes]
rs1255877	0.94[EUR][1000 genomes]
rs1255878	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1255879	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1255880	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1255881	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1255882	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1255883	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255885	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255887	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255890	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1255891	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1255892	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1255896	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255900	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255901	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255902	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255903	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1255905	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255908	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1262235	0.91[EUR][1000 genomes]
rs1262237	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1266870	0.95[EUR][1000 genomes]
rs1270526	0.95[EUR][1000 genomes]
rs1271567	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1272156	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1272714	0.90[EUR][1000 genomes]
rs1273192	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12878653	0.82[EUR][1000 genomes]
rs2184292	0.88[EUR][1000 genomes]
rs2357175	0.88[EUR][1000 genomes]
rs2792201	0.95[EUR][1000 genomes]
rs28483877	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884111	0.88[EUR][1000 genomes]
rs2994421	0.95[EUR][1000 genomes]
rs2994422	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35224808	0.84[EUR][1000 genomes]
rs61984073	0.86[EUR][1000 genomes]
rs7156570	0.88[EUR][1000 genomes]
rs8009321	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9323442	0.89[EUR][1000 genomes]
rs9323443	0.88[EUR][1000 genomes]
rs945027	0.95[EUR][1000 genomes]
rs945028	0.95[EUR][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	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
4	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
5	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
6	nsv902020	chr14:64434288-64506541	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10498512	SYNE2	cis	cerebellum	SCAN
rs10498512	KCNH5	cis	parietal	SCAN
rs10498512	C14orf39	cis	cerebellum	SCAN
rs10498512	DAAM1	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64395000-64491000	Weak transcription	Psoas Muscle	Psoas
2	chr14:64419200-64489000	Weak transcription	Small Intestine	intestine
3	chr14:64440800-64480400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr14:64442400-64491000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:64452400-64480600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr14:64452600-64479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr14:64457000-64474600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr14:64457000-64480000	Strong transcription	Dnd41	blood
9	chr14:64457000-64502000	Strong transcription	Placenta	Placenta
10	chr14:64457000-64519200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr14:64457200-64476000	Strong transcription	Fetal Brain Female	brain
12	chr14:64457200-64480200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr14:64458800-64490400	Weak transcription	Colonic Mucosa	Colon
14	chr14:64459600-64478800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:64459600-64481200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:64460000-64481200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr14:64460000-64488000	Weak transcription	Pancreas	Pancrea
18	chr14:64460000-64513400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr14:64460600-64495000	Weak transcription	NHDF-Ad	bronchial
20	chr14:64462600-64475800	Strong transcription	Fetal Intestine Large	intestine
21	chr14:64462600-64479000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr14:64462600-64479000	Strong transcription	Fetal Stomach	stomach
23	chr14:64462800-64476000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr14:64462800-64476200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr14:64463200-64491000	Weak transcription	Fetal Brain Male	brain
26	chr14:64463600-64475000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr14:64464000-64488600	Weak transcription	HUVEC	blood vessel
28	chr14:64465800-64475600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr14:64466400-64490600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr14:64466600-64490400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr14:64466600-64513200	Weak transcription	NHEK	skin
32	chr14:64466600-64593200	Weak transcription	Colon Smooth Muscle	Colon
33	chr14:64467800-64475800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr14:64468000-64475600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr14:64468000-64480600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:64468400-64482200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr14:64468800-64527200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr14:64469200-64488000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr14:64469400-64475600	Strong transcription	Brain Germinal Matrix	brain
40	chr14:64469600-64475600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr14:64469600-64518400	Weak transcription	HMEC	breast
42	chr14:64470000-64490600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr14:64470200-64475600	Strong transcription	Thymus	Thymus
44	chr14:64470200-64488000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr14:64470400-64475000	Strong transcription	Aorta	Aorta
46	chr14:64470400-64478200	Weak transcription	Fetal Thymus	thymus
47	chr14:64470400-64481000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr14:64470400-64481000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr14:64470400-64484400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr14:64470600-64478000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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