Variant report

Variant	rs9697261
Chromosome Location	chr9:94865656-94865657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94860200..94862194-chr9:94864408..94866012,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10115565	0.91[AFR][1000 genomes]
rs10116088	0.93[AFR][1000 genomes]
rs10117113	0.83[AFR][1000 genomes]
rs10117143	0.90[AFR][1000 genomes]
rs10117394	0.91[AFR][1000 genomes]
rs10118614	0.81[AFR][1000 genomes]
rs10118847	0.91[AFR][1000 genomes]
rs10119603	0.89[AFR][1000 genomes]
rs10121694	0.91[AFR][1000 genomes]
rs10122415	0.91[AFR][1000 genomes]
rs10122798	0.90[AFR][1000 genomes]
rs10123181	0.81[AFR][1000 genomes]
rs10123678	0.83[AFR][1000 genomes]
rs10124473	0.83[AFR][1000 genomes]
rs10992202	0.90[AFR][1000 genomes]
rs10992223	0.91[AFR][1000 genomes]
rs12336291	0.93[AFR][1000 genomes]
rs12336497	0.91[AFR][1000 genomes]
rs12336689	0.92[AFR][1000 genomes]
rs12338124	0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12341602	0.93[AFR][1000 genomes]
rs12341791	0.93[AFR][1000 genomes]
rs12343645	0.91[AFR][1000 genomes]
rs12343647	0.91[AFR][1000 genomes]
rs12344414	0.93[AFR][1000 genomes]
rs12347966	0.93[AFR][1000 genomes]
rs12348496	0.89[AFR][1000 genomes]
rs12349327	0.93[AFR][1000 genomes]
rs12352341	0.93[AFR][1000 genomes]
rs12353142	0.83[AFR][1000 genomes]
rs16908113	0.91[AFR][1000 genomes]
rs16908131	0.91[AFR][1000 genomes]
rs28391324	0.91[AFR][1000 genomes]
rs28429191	0.95[AFR][1000 genomes]
rs28437390	0.93[AFR][1000 genomes]
rs28504279	0.90[AFR][1000 genomes]
rs28505748	0.81[AFR][1000 genomes]
rs28513744	0.91[AFR][1000 genomes]
rs28552704	0.89[AFR][1000 genomes]
rs28637477	0.93[AFR][1000 genomes]
rs28744634	0.89[AFR][1000 genomes]
rs28759240	0.93[AFR][1000 genomes]
rs28819206	0.89[AFR][1000 genomes]
rs3858086	0.81[AFR][1000 genomes]
rs4344138	0.91[AFR][1000 genomes]
rs4498616	0.91[AFR][1000 genomes]
rs4560856	0.91[AFR][1000 genomes]
rs4604504	0.91[AFR][1000 genomes]
rs56204501	0.91[AFR][1000 genomes]
rs56208357	0.81[AFR][1000 genomes]
rs56248784	0.81[AFR][1000 genomes]
rs57496363	0.89[AFR][1000 genomes]
rs57862149	0.81[AFR][1000 genomes]
rs58224960	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58679317	0.89[AFR][1000 genomes]
rs59790820	0.91[AFR][1000 genomes]
rs60230478	0.92[AFR][1000 genomes]
rs60743157	0.91[AFR][1000 genomes]
rs61000917	0.93[AFR][1000 genomes]
rs61246786	0.81[AFR][1000 genomes]
rs61456615	0.91[AFR][1000 genomes]
rs7018595	0.91[AFR][1000 genomes]
rs7018827	0.91[AFR][1000 genomes]
rs7021285	0.81[AFR][1000 genomes]
rs7021408	0.91[AFR][1000 genomes]
rs7024215	0.91[AFR][1000 genomes]
rs7025703	0.93[AFR][1000 genomes]
rs7027257	0.81[AFR][1000 genomes]
rs7028378	0.83[AFR][1000 genomes]
rs7033888	0.88[AFR][1000 genomes]
rs7035964	0.91[AFR][1000 genomes]
rs7039366	0.83[AFR][1000 genomes]
rs7046206	0.91[AFR][1000 genomes]
rs73510406	0.83[AFR][1000 genomes]
rs73510411	0.81[AFR][1000 genomes]
rs73512337	0.81[AFR][1000 genomes]
rs73512378	0.93[AFR][1000 genomes]
rs73527329	0.83[AFR][1000 genomes]
rs73527330	0.91[AFR][1000 genomes]
rs73653014	0.91[AFR][1000 genomes]
rs7848959	0.91[AFR][1000 genomes]
rs7849664	0.83[AFR][1000 genomes]
rs7856188	0.89[AFR][1000 genomes]
rs7870339	0.93[AFR][1000 genomes]
rs7870565	0.91[AFR][1000 genomes]
rs7871565	0.91[AFR][1000 genomes]
rs7871997	0.91[AFR][1000 genomes]
rs9696251	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv972418	chr9:94865248-94870773	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9697261	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	chr9:94840600-94872000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:94842800-94866000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:94842800-94867600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:94842800-94876600	Weak transcription	Colonic Mucosa	Colon
7	chr9:94843000-94866000	Weak transcription	Lung	lung
8	chr9:94851400-94876600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:94851800-94866000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:94851800-94867600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:94857000-94875400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr9:94857200-94866200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:94857800-94866200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:94858200-94867600	Weak transcription	Brain Angular Gyrus	brain
15	chr9:94858200-94869000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr9:94858200-94873600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr9:94858400-94866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:94858400-94872200	Weak transcription	K562	blood
19	chr9:94858600-94869400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:94858800-94873400	Weak transcription	GM12878-XiMat	blood
21	chr9:94859000-94870000	Weak transcription	HepG2	liver
22	chr9:94859200-94867600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:94859600-94872800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:94860400-94872000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:94860800-94866000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr9:94860800-94872600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:94860800-94873600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:94860800-94876000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:94860800-94876000	Weak transcription	Brain Substantia Nigra	brain
30	chr9:94860800-94877000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:94860800-94877200	Weak transcription	Stomach Mucosa	stomach
32	chr9:94861000-94867600	Weak transcription	Fetal Thymus	thymus
33	chr9:94861000-94870600	Weak transcription	Primary B cells from cord blood	blood
34	chr9:94861000-94875000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr9:94861000-94876800	Weak transcription	Fetal Kidney	kidney
36	chr9:94861200-94865800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:94861200-94868800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr9:94861200-94876000	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:94861400-94873000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr9:94861400-94875600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr9:94861600-94866200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr9:94861600-94875800	Weak transcription	Fetal Brain Male	brain
43	chr9:94861600-94877000	Weak transcription	Small Intestine	intestine
44	chr9:94862600-94866200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr9:94863000-94866000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:94863000-94866000	Weak transcription	Gastric	stomach
47	chr9:94863000-94870200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:94863000-94873400	Weak transcription	NHLF	lung
49	chr9:94863000-94876800	Weak transcription	HSMMtube	muscle
50	chr9:94863200-94868800	Weak transcription	Dnd41	blood

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