Variant report

Variant	rs1884606
Chromosome Location	chr20:16312529-16312530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12624939	1.00[CHB][hapmap]
rs12625552	1.00[CHB][hapmap]
rs12625709	0.86[ASN][1000 genomes]
rs1590872	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1884603	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884604	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884605	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2093004	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144883	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144885	0.83[CHD][hapmap];0.82[AMR][1000 genomes]
rs2144886	0.83[CHD][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs2144887	1.00[JPT][hapmap]
rs2144891	0.83[CHD][hapmap]
rs2180442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2180443	0.83[CHD][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs2208057	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208058	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208059	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2328016	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2328017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328019	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]
rs2328020	0.83[CHD][hapmap]
rs4814469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814478	0.83[CHD][hapmap]
rs6034438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6034439	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6034446	1.00[CHB][hapmap]
rs6034447	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs6034453	0.86[ASN][1000 genomes]
rs6034460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6034461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034464	0.83[CHD][hapmap]
rs6034487	1.00[CHB][hapmap]
rs6043852	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043854	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043858	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043870	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043879	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043881	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043882	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6043892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043904	0.88[GIH][hapmap]
rs6043911	0.83[CHD][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs6043913	0.82[AMR][1000 genomes]
rs6075048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075051	0.82[AMR][1000 genomes]
rs6080229	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080243	1.00[JPT][hapmap]
rs6105582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6105603	1.00[CHB][hapmap]
rs6111060	0.85[GIH][hapmap]
rs6111075	0.83[CHD][hapmap]
rs6135739	0.83[CHD][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs7271622	1.00[CHB][hapmap]
rs8117949	1.00[CHB][hapmap]
rs8119246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8122535	1.00[CHB][hapmap]
rs913826	0.82[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.90[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
rs1884606	SPTLC3	cis	cerebellum	SCAN

Chromatin state (count:62 , 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	chr20:16284400-16313600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr20:16284600-16313600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:16285400-16330000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:16287000-16315200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr20:16288000-16332400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:16288400-16318200	Weak transcription	Pancreas	Pancrea
9	chr20:16288800-16313800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr20:16288800-16318600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr20:16289200-16313800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr20:16289400-16348000	Weak transcription	Colonic Mucosa	Colon
13	chr20:16289800-16323200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:16290000-16313600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr20:16290400-16313800	Weak transcription	Spleen	Spleen
16	chr20:16291200-16312800	Weak transcription	Aorta	Aorta
17	chr20:16291200-16313600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr20:16291200-16314400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr20:16291200-16317800	Weak transcription	Esophagus	oesophagus
20	chr20:16291400-16331000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr20:16293200-16314800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr20:16294000-16318200	Weak transcription	Fetal Stomach	stomach
23	chr20:16295600-16313600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr20:16295600-16318600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:16295600-16349000	Weak transcription	HepG2	liver
26	chr20:16295800-16315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr20:16296200-16315400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr20:16296600-16313800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr20:16296600-16345200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr20:16296800-16318200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr20:16298600-16313400	Weak transcription	Ovary	ovary
32	chr20:16298800-16333400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr20:16299200-16313000	Weak transcription	Adipose Nuclei	Adipose
34	chr20:16301200-16317400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr20:16301600-16314000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr20:16302800-16313600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr20:16302800-16330600	Weak transcription	Brain Substantia Nigra	brain
38	chr20:16303000-16313800	Weak transcription	Brain Hippocampus Middle	brain
39	chr20:16305200-16313600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr20:16306600-16328400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr20:16307000-16316600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr20:16307200-16313600	Weak transcription	Primary B cells from cord blood	blood
43	chr20:16307600-16313800	Weak transcription	Fetal Intestine Large	intestine
44	chr20:16308400-16329400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr20:16309000-16319400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr20:16309200-16316800	Weak transcription	Fetal Heart	heart
47	chr20:16309800-16313600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr20:16309800-16313600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr20:16309800-16326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr20:16310200-16313600	Weak transcription	Liver	Liver

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