Variant report

Variant	rs28513744
Chromosome Location	chr9:94818586-94818587
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94770078..94772995-chr9:94817717..94819222,2	K562	blood:
2	chr9:94811198..94813867-chr9:94816411..94819240,2	MCF-7	breast:

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10115181	0.95[ASN][1000 genomes]
rs10115565	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10116088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117113	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10117143	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118614	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10118847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119603	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10119983	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121430	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121694	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121928	0.85[EUR][1000 genomes]
rs10122415	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122798	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123181	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10123678	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10124473	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10124705	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10992194	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992202	0.99[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10992223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336291	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336689	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12338124	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12341602	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12341791	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344414	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345896	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12347966	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12348496	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12349001	0.85[EUR][1000 genomes]
rs12349327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12353142	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12353321	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908106	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16908113	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28391324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429191	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437390	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477960	0.85[EUR][1000 genomes]
rs28504279	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28505748	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28552704	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28637477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28735483	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28744634	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28759240	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804693	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28819206	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28825409	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28883017	0.95[ASN][1000 genomes]
rs3858086	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4302907	0.95[ASN][1000 genomes]
rs4344138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56204501	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56208357	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56248784	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56266486	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57496363	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57862149	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs58224960	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58679317	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs59790820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60230478	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60743157	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61000917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61246786	0.89[AFR][1000 genomes]
rs61456615	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61596207	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6479397	0.90[ASN][1000 genomes]
rs7018595	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018827	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021285	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7021293	0.90[ASN][1000 genomes]
rs7021408	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025703	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027257	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7028378	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7033888	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7034509	1.00[ASN][1000 genomes]
rs7035964	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7039366	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7045602	0.86[AMR][1000 genomes]
rs7046206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047389	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73510406	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73510411	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73512337	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73512339	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73512378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73522907	0.85[EUR][1000 genomes]
rs73522929	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73527329	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73527330	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73653014	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7848959	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7849664	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7851249	0.90[ASN][1000 genomes]
rs7851412	0.85[EUR][1000 genomes]
rs7852989	0.95[ASN][1000 genomes]
rs7856188	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7864340	0.95[ASN][1000 genomes]
rs7865994	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7867659	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7870339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871997	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7872238	1.00[ASN][1000 genomes]
rs9696251	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9697261	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv982320	chr9:94799706-94821700	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28513744	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94803400-94821200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:94805000-94823200	Strong transcription	Duodenum Mucosa	Duodenum
3	chr9:94805400-94821600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:94805600-94822600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:94805600-94823400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:94805800-94821200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:94805800-94822800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:94806000-94823200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr9:94806800-94822000	Weak transcription	Stomach Mucosa	stomach
10	chr9:94806800-94822400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr9:94806800-94822800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr9:94807200-94822000	Weak transcription	Psoas Muscle	Psoas
13	chr9:94807200-94822600	Strong transcription	Primary T cells from cord blood	blood
14	chr9:94807200-94823000	Strong transcription	Primary B cells from cord blood	blood
15	chr9:94807200-94823200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr9:94807400-94822800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:94807600-94824600	Weak transcription	Fetal Brain Male	brain
18	chr9:94809600-94818800	Weak transcription	HMEC	breast
19	chr9:94809600-94820600	Weak transcription	Pancreas	Pancrea
20	chr9:94809600-94823600	Weak transcription	Colonic Mucosa	Colon
21	chr9:94810000-94818800	Weak transcription	NHDF-Ad	bronchial
22	chr9:94810000-94820600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:94810800-94860200	Weak transcription	Right Ventricle	heart
24	chr9:94811200-94822600	Strong transcription	Primary hematopoietic stem cells	blood
25	chr9:94811800-94828400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:94812200-94822400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:94812200-94832200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:94812400-94828400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:94812800-94819800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:94813000-94818800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr9:94814200-94819000	Strong transcription	Liver	Liver
32	chr9:94814400-94819200	Strong transcription	Fetal Intestine Large	intestine
33	chr9:94814800-94822000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:94815200-94818600	Strong transcription	NHEK	skin
35	chr9:94815200-94819800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:94815400-94818800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:94815400-94819000	Strong transcription	Thymus	Thymus
38	chr9:94815400-94819400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:94815400-94819600	Strong transcription	GM12878-XiMat	blood
40	chr9:94815400-94820000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr9:94815400-94820600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr9:94815400-94822200	Strong transcription	Fetal Muscle Leg	muscle
43	chr9:94815400-94822600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr9:94815400-94822600	Strong transcription	Placenta	Placenta
45	chr9:94815400-94823000	Strong transcription	Dnd41	blood
46	chr9:94815600-94818800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr9:94815600-94819600	Strong transcription	Adipose Nuclei	Adipose
48	chr9:94815600-94819800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr9:94815600-94821200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:94815600-94821400	Strong transcription	Rectal Mucosa Donor 29	rectum

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