Variant report

Variant	rs12336291
Chromosome Location	chr9:94859352-94859353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:117549422..117551899-chr9:94857781..94859628,2	MCF-7	breast:
2	chr9:94850893..94855871-chr9:94857090..94860833,5	K562	blood:
3	chr9:94849623..94853423-chr9:94859037..94861746,3	MCF-7	breast:
4	chr9:94853798..94856024-chr9:94859327..94862395,3	MCF-7	breast:

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10115181	0.95[ASN][1000 genomes]
rs10115565	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10116088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117113	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10117143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117394	0.98[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	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10118847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119603	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10119983	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121430	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121694	0.98[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	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122798	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123181	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10123678	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10124473	0.86[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	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10992223	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336497	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336689	0.99[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12341791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343645	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344414	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345896	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12347966	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12348496	0.96[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12353142	0.90[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	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16908113	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28391324	0.98[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]
rs28437390	0.96[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	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28513744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28552704	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28637477	0.96[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	0.96[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	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28819206	0.96[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	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4302907	0.95[ASN][1000 genomes]
rs4344138	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498616	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604504	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56204501	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56208357	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56248784	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56266486	0.92[EUR][1000 genomes]
rs57496363	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57862149	0.88[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	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59790820	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60230478	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60743157	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61000917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61246786	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61456615	0.98[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	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018827	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021285	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7021293	0.90[ASN][1000 genomes]
rs7021408	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027257	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7028378	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7033888	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7034509	1.00[ASN][1000 genomes]
rs7035964	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7039366	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7045602	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7046206	0.98[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	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73510411	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73512337	0.87[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	1.00[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	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73527329	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73527330	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73653014	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7848959	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7849664	0.90[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	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7864340	0.95[ASN][1000 genomes]
rs7865994	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7867659	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7870339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870565	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871565	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871997	0.98[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: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	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
rs12336291	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94810800-94860200	Weak transcription	Right Ventricle	heart
2	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
3	chr9:94822400-94860200	Weak transcription	Stomach Mucosa	stomach
4	chr9:94824000-94860400	Weak transcription	Psoas Muscle	Psoas
5	chr9:94829000-94862600	Weak transcription	Hela-S3	cervix
6	chr9:94830200-94860400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:94830800-94873800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:94839400-94861000	Weak transcription	HMEC	breast
9	chr9:94840200-94865400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:94840600-94872000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr9:94842200-94860400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:94842200-94860400	Weak transcription	Pancreas	Pancrea
13	chr9:94842200-94860600	Weak transcription	Aorta	Aorta
14	chr9:94842200-94862400	Weak transcription	Esophagus	oesophagus
15	chr9:94842400-94860400	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:94842400-94861000	Weak transcription	Small Intestine	intestine
17	chr9:94842800-94860200	Weak transcription	Brain Germinal Matrix	brain
18	chr9:94842800-94866000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:94842800-94867600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr9:94842800-94876600	Weak transcription	Colonic Mucosa	Colon
21	chr9:94843000-94866000	Weak transcription	Lung	lung
22	chr9:94843400-94860200	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:94843400-94860400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:94844000-94860600	Weak transcription	Spleen	Spleen
25	chr9:94844000-94861000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:94844200-94860200	Weak transcription	NHEK	skin
27	chr9:94850400-94860000	Weak transcription	Fetal Brain Female	brain
28	chr9:94850800-94860400	Weak transcription	Ovary	ovary
29	chr9:94851200-94859800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:94851200-94860000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:94851200-94860600	Weak transcription	Fetal Brain Male	brain
32	chr9:94851400-94859400	Weak transcription	HSMM	muscle
33	chr9:94851400-94860000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:94851400-94860200	Weak transcription	Primary T cells from cord blood	blood
35	chr9:94851400-94860200	Weak transcription	Fetal Kidney	kidney
36	chr9:94851400-94860200	Weak transcription	Osteobl	bone
37	chr9:94851400-94860400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:94851400-94860400	Weak transcription	Liver	Liver
39	chr9:94851400-94860400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:94851400-94860400	Weak transcription	Gastric	stomach
41	chr9:94851400-94860600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:94851400-94860800	Weak transcription	NH-A	brain
43	chr9:94851400-94862400	Weak transcription	HSMMtube	muscle
44	chr9:94851400-94862600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:94851400-94862600	Weak transcription	Dnd41	blood
46	chr9:94851400-94862600	Weak transcription	NHLF	lung
47	chr9:94851400-94864000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr9:94851400-94864400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:94851400-94865400	Weak transcription	Thymus	Thymus
50	chr9:94851400-94876600	Weak transcription	H9 Cell Line	embryonic stem cell

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