Variant report

Variant	rs2328020
Chromosome Location	chr20:16349671-16349672
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12624939	1.00[JPT][hapmap]
rs1884598	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1884604	0.83[CHD][hapmap]
rs1884606	0.83[CHD][hapmap]
rs2144883	0.83[CHD][hapmap]
rs2144885	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144886	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144887	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144888	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144889	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144890	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144891	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2180442	1.00[JPT][hapmap]
rs2180443	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208056	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2876428	0.83[EUR][1000 genomes]
rs4814477	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814478	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814482	0.82[GIH][hapmap];0.88[MKK][hapmap];0.84[EUR][1000 genomes]
rs6034464	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034466	0.89[ASW][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6043882	0.83[CHD][hapmap]
rs6043911	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6043913	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6075051	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6080240	0.85[EUR][1000 genomes]
rs6080243	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6080244	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6105582	1.00[JPT][hapmap]
rs6105603	1.00[JPT][hapmap]
rs6111075	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6111076	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6135738	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6135739	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7268027	1.00[JPT][hapmap]
rs7271622	1.00[JPT][hapmap]
rs7272048	1.00[JPT][hapmap]
rs8117949	1.00[JPT][hapmap]
rs8122535	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833931	chr20:16308276-16460596	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2328020	SPTLC3	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16315400-16364400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr20:16315800-16357600	Weak transcription	Right Ventricle	heart
3	chr20:16316000-16384400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr20:16318800-16368200	Weak transcription	Primary B cells from cord blood	blood
5	chr20:16334000-16377400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:16341200-16371600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr20:16342600-16377400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr20:16342800-16349800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr20:16343600-16366800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr20:16343600-16384600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr20:16343800-16351800	Weak transcription	HSMM	muscle
12	chr20:16343800-16356800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr20:16344000-16350600	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr20:16344000-16352400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr20:16344400-16380200	Weak transcription	HSMMtube	muscle
16	chr20:16344800-16359400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr20:16344800-16360800	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr20:16344800-16371400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr20:16344800-16377400	Weak transcription	Brain Angular Gyrus	brain
20	chr20:16345000-16349800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr20:16345000-16351200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr20:16345000-16351200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr20:16345000-16391200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr20:16345200-16349800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr20:16345200-16350600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr20:16345200-16359400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr20:16345400-16353200	Strong transcription	Adipose Nuclei	Adipose
28	chr20:16345400-16377400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr20:16345400-16391000	Weak transcription	Brain Germinal Matrix	brain
30	chr20:16345800-16351000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:16346000-16351200	Strong transcription	Liver	Liver
32	chr20:16346200-16350600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr20:16346200-16350600	Strong transcription	Lung	lung
34	chr20:16346200-16350800	Strong transcription	NHEK	skin
35	chr20:16346200-16351000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr20:16346200-16359200	Weak transcription	Fetal Brain Female	brain
37	chr20:16346400-16363200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr20:16346600-16351600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr20:16346600-16354600	Weak transcription	Aorta	Aorta
40	chr20:16346600-16362400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr20:16346600-16393600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr20:16346800-16350600	Strong transcription	Primary T cells from cord blood	blood
43	chr20:16346800-16359600	Weak transcription	Placenta	Placenta
44	chr20:16347200-16349800	Strong transcription	Brain Anterior Caudate	brain
45	chr20:16347200-16350000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr20:16347200-16351200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr20:16347200-16368200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr20:16347400-16360000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr20:16347600-16392000	Weak transcription	Fetal Kidney	kidney
50	chr20:16347800-16350400	Weak transcription	Hela-S3	cervix

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