Variant report

Variant	rs28437390
Chromosome Location	chr9:94872266-94872267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94871544..94874605-chr9:94874619..94877875,5	MCF-7	breast:
2	chr9:94867851..94872295-chr9:94876110..94878962,5	MCF-7	breast:
3	chr9:94871412..94875028-chr9:94875797..94879228,6	K562	blood:

Variant related genes	Relation type
ENSG00000090054	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10115181	0.95[ASN][1000 genomes]
rs10115565	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10116088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117113	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10117143	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117394	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118409	0.82[EUR][1000 genomes]
rs10118614	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10118847	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119603	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10119983	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121430	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121694	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121928	0.92[EUR][1000 genomes]
rs10122415	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122798	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123181	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10123678	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10124473	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10124705	0.92[EUR][1000 genomes]
rs10992194	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992202	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10992223	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336291	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336497	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336689	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12338124	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12341602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12341791	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343645	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343647	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345896	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12347966	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12348496	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12349001	0.92[EUR][1000 genomes]
rs12349327	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352341	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12353142	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12353321	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908106	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16908113	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908131	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28391324	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429191	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477960	0.92[EUR][1000 genomes]
rs28504279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28505748	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28513744	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28552704	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28637477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28735483	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28744634	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28759240	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804693	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28819206	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28825409	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28883017	0.95[ASN][1000 genomes]
rs3858086	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4302907	0.95[ASN][1000 genomes]
rs4344138	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498616	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560856	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604504	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56204501	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56208357	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56248784	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56266486	0.92[EUR][1000 genomes]
rs57496363	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57862149	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs58224960	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58679317	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59790820	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60230478	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60743157	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61000917	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61246786	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61456615	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61596207	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6479397	0.90[ASN][1000 genomes]
rs7018595	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018827	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021285	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7021293	0.90[ASN][1000 genomes]
rs7021408	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024215	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025703	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027257	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7028378	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7033888	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7034509	1.00[ASN][1000 genomes]
rs7035964	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7039366	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7045602	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7046206	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047389	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73510406	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73510411	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73512337	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73512339	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73512378	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73522907	0.92[EUR][1000 genomes]
rs73522929	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73527329	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73527330	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73653014	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7848959	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7849664	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7851249	0.90[ASN][1000 genomes]
rs7851412	0.92[EUR][1000 genomes]
rs7852989	0.95[ASN][1000 genomes]
rs7856188	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7864340	0.95[ASN][1000 genomes]
rs7865994	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7867659	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7870339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871997	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7872238	1.00[ASN][1000 genomes]
rs9696251	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9697261	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28437390	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
2	chr9:94830800-94873800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:94842800-94876600	Weak transcription	Colonic Mucosa	Colon
4	chr9:94851400-94876600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:94857000-94875400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr9:94858200-94873600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr9:94858800-94873400	Weak transcription	GM12878-XiMat	blood
8	chr9:94859600-94872800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:94860800-94872600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr9:94860800-94873600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:94860800-94876000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:94860800-94876000	Weak transcription	Brain Substantia Nigra	brain
13	chr9:94860800-94877000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:94860800-94877200	Weak transcription	Stomach Mucosa	stomach
15	chr9:94861000-94875000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr9:94861000-94876800	Weak transcription	Fetal Kidney	kidney
17	chr9:94861200-94876000	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:94861400-94873000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr9:94861400-94875600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:94861600-94875800	Weak transcription	Fetal Brain Male	brain
21	chr9:94861600-94877000	Weak transcription	Small Intestine	intestine
22	chr9:94863000-94873400	Weak transcription	NHLF	lung
23	chr9:94863000-94876800	Weak transcription	HSMMtube	muscle
24	chr9:94863200-94873600	Weak transcription	Psoas Muscle	Psoas
25	chr9:94863200-94876800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:94863400-94872600	Weak transcription	HUVEC	blood vessel
27	chr9:94863400-94873000	Weak transcription	HSMM	muscle
28	chr9:94863400-94873200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:94863600-94875800	Weak transcription	NHEK	skin
30	chr9:94864000-94875200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr9:94864200-94876000	Weak transcription	Hela-S3	cervix
32	chr9:94864400-94875000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:94864400-94875000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:94864600-94873000	Weak transcription	Brain Anterior Caudate	brain
35	chr9:94864600-94875600	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:94864600-94876800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:94864800-94875000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:94864800-94876200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:94865400-94872800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:94865400-94874600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:94865400-94874800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:94865600-94872600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr9:94865600-94874800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr9:94865600-94875000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:94865600-94875400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr9:94866000-94873600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr9:94866200-94874400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr9:94866200-94874800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr9:94866200-94875000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:94866200-94876600	Weak transcription	Rectal Smooth Muscle	rectum

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