Variant report

Variant	rs2328019
Chromosome Location	chr20:16327825-16327826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12625709	0.86[ASN][1000 genomes]
rs1590872	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1884603	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884604	0.82[ASW][hapmap];0.95[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884605	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884606	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093004	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144883	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144886	0.85[MEX][hapmap]
rs2144887	1.00[JPT][hapmap]
rs2180442	1.00[CEU][hapmap];0.88[GIH][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2180443	0.85[MEX][hapmap]
rs2208057	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208058	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208059	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2328016	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2328017	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328018	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814469	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814482	0.81[TSI][hapmap]
rs6034438	1.00[JPT][hapmap]
rs6034439	1.00[JPT][hapmap]
rs6034447	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs6034453	0.86[ASN][1000 genomes]
rs6034460	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6034461	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043852	1.00[JPT][hapmap]
rs6043854	1.00[JPT][hapmap]
rs6043858	1.00[JPT][hapmap]
rs6043870	1.00[JPT][hapmap]
rs6043879	1.00[JPT][hapmap]
rs6043881	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043882	0.81[ASW][hapmap];0.95[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043887	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6043892	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043904	0.85[GIH][hapmap]
rs6043911	0.85[MEX][hapmap]
rs6075048	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080229	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080243	1.00[JPT][hapmap]
rs6105582	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6111060	0.82[GIH][hapmap]
rs6135739	0.85[MEX][hapmap]
rs8119246	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913826	0.82[ASW][hapmap];0.95[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]

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
rs2328019	SPTLC3	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16262600-16346200	Weak transcription	Gastric	stomach
2	chr20:16276400-16348200	Weak transcription	Colon Smooth Muscle	Colon
3	chr20:16285400-16330000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:16288000-16332400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr20:16289400-16348000	Weak transcription	Colonic Mucosa	Colon
6	chr20:16291400-16331000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr20:16295600-16349000	Weak transcription	HepG2	liver
8	chr20:16296600-16345200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:16298800-16333400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr20:16302800-16330600	Weak transcription	Brain Substantia Nigra	brain
11	chr20:16306600-16328400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr20:16308400-16329400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr20:16311800-16329000	Weak transcription	Psoas Muscle	Psoas
14	chr20:16312400-16331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr20:16314000-16329600	Weak transcription	Lung	lung
16	chr20:16314600-16328800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr20:16315400-16330600	Weak transcription	Brain Hippocampus Middle	brain
18	chr20:16315400-16331000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:16315400-16345000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr20:16315400-16346200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr20:16315400-16348000	Weak transcription	Fetal Intestine Large	intestine
22	chr20:16315400-16364400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr20:16315600-16329600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr20:16315600-16329800	Weak transcription	Fetal Muscle Leg	muscle
25	chr20:16315600-16331000	Weak transcription	Aorta	Aorta
26	chr20:16315600-16346200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr20:16315600-16348000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr20:16315600-16348400	Weak transcription	Spleen	Spleen
29	chr20:16315800-16357600	Weak transcription	Right Ventricle	heart
30	chr20:16316000-16329600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr20:16316000-16332000	Weak transcription	Brain Anterior Caudate	brain
32	chr20:16316000-16344000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr20:16316000-16346200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr20:16316000-16384400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr20:16316200-16347200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr20:16316600-16330800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr20:16318600-16346200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr20:16318600-16348400	Weak transcription	Esophagus	oesophagus
39	chr20:16318800-16345000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr20:16318800-16368200	Weak transcription	Primary B cells from cord blood	blood
41	chr20:16319000-16329600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr20:16319000-16345800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr20:16319000-16346200	Weak transcription	Pancreas	Pancrea
44	chr20:16319000-16346400	Weak transcription	Fetal Intestine Small	intestine
45	chr20:16320600-16336600	Weak transcription	Primary T cells from cord blood	blood
46	chr20:16322600-16346000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr20:16326200-16346000	Weak transcription	Liver	Liver
48	chr20:16326600-16330800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr20:16327000-16330800	Weak transcription	HSMMtube	muscle
50	chr20:16327000-16332800	Weak transcription	Fetal Stomach	stomach

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