Variant report

Variant	rs1255905
Chromosome Location	chr14:64456827-64456828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10149728	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10498512	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873172	0.83[CEU][hapmap];0.80[CHB][hapmap]
rs11623650	0.88[EUR][1000 genomes]
rs12147217	0.81[CHB][hapmap]
rs1255856	0.87[EUR][1000 genomes]
rs1255867	0.96[EUR][1000 genomes]
rs1255869	0.96[EUR][1000 genomes]
rs1255872	0.96[EUR][1000 genomes]
rs1255873	0.96[EUR][1000 genomes]
rs1255874	0.96[EUR][1000 genomes]
rs1255875	0.96[EUR][1000 genomes]
rs1255876	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1255877	0.95[EUR][1000 genomes]
rs1255878	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255879	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255880	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255881	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1255882	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1255883	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255885	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255887	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255890	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255891	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255892	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255896	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255900	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255901	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255902	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255903	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255908	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1262235	0.92[EUR][1000 genomes]
rs1262237	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1266870	0.96[EUR][1000 genomes]
rs1270526	0.96[EUR][1000 genomes]
rs1271567	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1272156	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1272714	0.91[EUR][1000 genomes]
rs1273192	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12878653	0.82[EUR][1000 genomes]
rs2184292	0.88[EUR][1000 genomes]
rs2357175	0.88[EUR][1000 genomes]
rs2357176	0.80[EUR][1000 genomes]
rs2792201	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28483877	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2884111	0.88[EUR][1000 genomes]
rs2994421	0.96[EUR][1000 genomes]
rs2994422	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35224808	0.85[EUR][1000 genomes]
rs61984073	0.87[EUR][1000 genomes]
rs7156570	0.88[EUR][1000 genomes]
rs8009321	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9323442	0.89[EUR][1000 genomes]
rs9323443	0.88[EUR][1000 genomes]
rs945027	0.96[EUR][1000 genomes]
rs945028	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1255905	C14orf39	cis	cerebellum	SCAN
rs1255905	DAAM1	cis	cerebellum	SCAN
rs1255905	SYNE2	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	chr14:64416800-64458600	Weak transcription	Gastric	stomach
3	chr14:64417000-64459200	Weak transcription	NHEK	skin
4	chr14:64417000-64466000	Weak transcription	Colon Smooth Muscle	Colon
5	chr14:64417200-64458600	Weak transcription	Esophagus	oesophagus
6	chr14:64417400-64466200	Weak transcription	Right Ventricle	heart
7	chr14:64417600-64459200	Weak transcription	Pancreas	Pancrea
8	chr14:64418000-64463000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:64418400-64458600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:64419000-64463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:64419200-64489000	Weak transcription	Small Intestine	intestine
12	chr14:64419400-64459000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr14:64419400-64459200	Weak transcription	HMEC	breast
14	chr14:64420000-64458000	Weak transcription	Colonic Mucosa	Colon
15	chr14:64420200-64459000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr14:64420600-64462600	Weak transcription	HUVEC	blood vessel
17	chr14:64421600-64466000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr14:64423800-64463000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:64428400-64459400	Weak transcription	Aorta	Aorta
20	chr14:64429600-64458000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr14:64431000-64458200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr14:64431200-64463800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr14:64431200-64464800	Weak transcription	Stomach Mucosa	stomach
24	chr14:64432800-64457200	Weak transcription	Fetal Thymus	thymus
25	chr14:64433400-64465800	Weak transcription	Fetal Heart	heart
26	chr14:64434800-64458600	Weak transcription	Lung	lung
27	chr14:64435200-64457600	Weak transcription	Adipose Nuclei	Adipose
28	chr14:64435200-64458200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr14:64435200-64471800	Weak transcription	Hela-S3	cervix
30	chr14:64435400-64463600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr14:64439200-64465600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr14:64439600-64462800	Weak transcription	Fetal Brain Male	brain
33	chr14:64439800-64467800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr14:64440000-64457200	Weak transcription	Fetal Brain Female	brain
35	chr14:64440800-64466000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr14:64440800-64480400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr14:64441600-64467600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr14:64442400-64491000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr14:64442800-64458400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr14:64443000-64457600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr14:64443200-64458400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr14:64443600-64458200	Weak transcription	Primary B cells from cord blood	blood
43	chr14:64444800-64457600	Weak transcription	Primary T cells from cord blood	blood
44	chr14:64445000-64457200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr14:64445000-64457600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr14:64445000-64457600	Weak transcription	Liver	Liver
47	chr14:64445000-64457600	Weak transcription	Fetal Kidney	kidney
48	chr14:64445200-64459600	Weak transcription	Ovary	ovary
49	chr14:64445800-64458000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr14:64445800-64463800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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