Variant report

Variant	rs6573536
Chromosome Location	chr14:64342520-64342521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1000904	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873171	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11158515	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs11158518	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs11626911	0.82[CHB][hapmap]
rs11628650	0.87[CHB][hapmap]
rs12431956	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs12435958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12436656	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12586461	0.80[ASN][1000 genomes]
rs12587452	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12893838	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12894053	0.80[CEU][hapmap]
rs1959034	0.90[MEX][hapmap]
rs2151763	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357003	0.90[MEX][hapmap]
rs34486661	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35234298	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36050513	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902251	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902252	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4902253	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs55925976	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61985747	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573532	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573533	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67011590	0.80[ASN][1000 genomes]
rs7140278	0.80[ASN][1000 genomes]
rs7143794	0.80[ASN][1000 genomes]
rs7144370	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7145302	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7145810	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7146821	0.90[MEX][hapmap]
rs7149405	0.80[ASN][1000 genomes]
rs7149609	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7150540	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7153723	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7158960	0.90[ASN][1000 genomes]
rs7161586	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8004989	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8009846	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8010094	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8010312	0.82[CHB][hapmap]
rs8013611	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs8015158	0.81[AFR][1000 genomes]
rs8015354	0.81[AFR][1000 genomes]
rs8017009	0.87[CHB][hapmap]
rs945031	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs951250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs998242	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6573536	FLJ43390	cis	cerebellum	SCAN
rs6573536	SYT16	cis	parietal	SCAN
rs6573536	SYNE2	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64321400-64350200	Weak transcription	Fetal Stomach	stomach
2	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr14:64327600-64360000	Weak transcription	Gastric	stomach
4	chr14:64330200-64343600	Weak transcription	Brain Germinal Matrix	brain
5	chr14:64331200-64356400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr14:64335200-64360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:64336800-64362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr14:64337000-64343600	Weak transcription	Fetal Intestine Large	intestine
9	chr14:64337000-64357200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr14:64337000-64365200	Weak transcription	Fetal Thymus	thymus
11	chr14:64337600-64342600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr14:64337600-64343600	Weak transcription	A549	lung
13	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
14	chr14:64338000-64353800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr14:64338000-64355200	Weak transcription	Primary B cells from cord blood	blood
16	chr14:64339400-64366800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr14:64340000-64342800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr14:64340200-64342800	Enhancers	Adipose Nuclei	Adipose
19	chr14:64340200-64344000	Enhancers	Left Ventricle	heart
20	chr14:64340400-64342800	Enhancers	Ovary	ovary
21	chr14:64340400-64343000	Enhancers	Fetal Heart	heart
22	chr14:64340400-64343600	Enhancers	Right Atrium	heart
23	chr14:64340400-64345600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr14:64340600-64342600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr14:64340600-64342800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr14:64340600-64343000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr14:64340600-64343600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr14:64340600-64343800	Enhancers	Psoas Muscle	Psoas
29	chr14:64340600-64345000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr14:64340600-64345200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr14:64340800-64342600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr14:64340800-64342800	Enhancers	Hela-S3	cervix
33	chr14:64341000-64342600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr14:64341000-64342600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr14:64341000-64342800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr14:64341000-64343000	Enhancers	NHEK	skin
37	chr14:64341000-64356400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr14:64341000-64357200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:64341200-64344000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr14:64341200-64345000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr14:64341200-64346200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr14:64341200-64348400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr14:64341200-64348600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr14:64341200-64348800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr14:64341200-64351000	Weak transcription	Right Ventricle	heart
46	chr14:64341200-64352200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr14:64341200-64352400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr14:64341200-64354000	Weak transcription	Dnd41	blood
49	chr14:64341200-64354800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr14:64341200-64356400	Weak transcription	H1 Cell Line	embryonic stem cell

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