Variant report

Variant	rs1255887
Chromosome Location	chr14:64430267-64430268
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10149728	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10498512	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873172	0.87[ASW][hapmap];0.91[CEU][hapmap];0.80[CHB][hapmap];0.85[YRI][hapmap]
rs11623650	0.90[EUR][1000 genomes]
rs12147217	0.81[CHB][hapmap]
rs1255856	0.91[EUR][1000 genomes]
rs1255857	0.81[EUR][1000 genomes]
rs1255867	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1255869	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1255872	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255873	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1255874	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255875	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255876	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255877	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1255878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255881	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1255882	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1255883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255885	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255890	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255891	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255892	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255896	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255900	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255901	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255902	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255903	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255905	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255908	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1262235	0.94[EUR][1000 genomes]
rs1262237	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1266870	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1270526	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1271567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1272156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1272714	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1273192	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12878653	0.84[EUR][1000 genomes]
rs12881652	0.80[EUR][1000 genomes]
rs2184292	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2357175	0.93[EUR][1000 genomes]
rs2357176	0.84[EUR][1000 genomes]
rs2792201	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28483877	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2884111	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2994421	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2994422	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35224808	0.89[EUR][1000 genomes]
rs61984073	0.91[EUR][1000 genomes]
rs7156570	0.93[EUR][1000 genomes]
rs8009321	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9323442	0.91[EUR][1000 genomes]
rs9323443	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs945027	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs945028	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1255887	SYNE2	cis	cerebellum	SCAN
rs1255887	DAAM1	cis	cerebellum	SCAN
rs1255887	C14orf39	cis	cerebellum	SCAN
rs1255887	KCNH5	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64395000-64491000	Weak transcription	Psoas Muscle	Psoas
2	chr14:64403600-64432800	Weak transcription	Lung	lung
3	chr14:64406200-64434400	Weak transcription	Hela-S3	cervix
4	chr14:64408200-64432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:64414400-64439600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:64415400-64435800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr14:64415600-64439000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr14:64416800-64458600	Weak transcription	Gastric	stomach
9	chr14:64417000-64430800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr14:64417000-64459200	Weak transcription	NHEK	skin
11	chr14:64417000-64466000	Weak transcription	Colon Smooth Muscle	Colon
12	chr14:64417200-64458600	Weak transcription	Esophagus	oesophagus
13	chr14:64417400-64466200	Weak transcription	Right Ventricle	heart
14	chr14:64417600-64459200	Weak transcription	Pancreas	Pancrea
15	chr14:64418000-64435000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr14:64418000-64463000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:64418200-64450800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr14:64418400-64458600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr14:64419000-64432200	Weak transcription	Fetal Thymus	thymus
20	chr14:64419000-64432800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr14:64419000-64433000	Weak transcription	Fetal Intestine Small	intestine
22	chr14:64419000-64463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr14:64419200-64432000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr14:64419200-64438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr14:64419200-64489000	Weak transcription	Small Intestine	intestine
26	chr14:64419400-64448200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr14:64419400-64459000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr14:64419400-64459200	Weak transcription	HMEC	breast
29	chr14:64420000-64458000	Weak transcription	Colonic Mucosa	Colon
30	chr14:64420200-64432200	Weak transcription	Spleen	Spleen
31	chr14:64420200-64432200	Weak transcription	GM12878-XiMat	blood
32	chr14:64420200-64433800	Weak transcription	Brain Germinal Matrix	brain
33	chr14:64420200-64442400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:64420200-64459000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr14:64420600-64432000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr14:64420600-64462600	Weak transcription	HUVEC	blood vessel
37	chr14:64421600-64466000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr14:64423400-64444400	Weak transcription	Liver	Liver
39	chr14:64423600-64431800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr14:64423600-64431800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr14:64423600-64434000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr14:64423800-64444400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr14:64423800-64463000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr14:64424000-64431800	Weak transcription	Ovary	ovary
45	chr14:64424600-64432000	Weak transcription	Adipose Nuclei	Adipose
46	chr14:64424800-64431600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr14:64425400-64432200	Weak transcription	Fetal Intestine Large	intestine
48	chr14:64425400-64433000	Weak transcription	Fetal Muscle Leg	muscle
49	chr14:64425600-64434000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr14:64426800-64440000	Strong transcription	Placenta	Placenta

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