Variant report

Variant	rs61596207
Chromosome Location	chr9:94878946-94878947
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr9:94878692-94878979	GM12878	blood:	n/a	n/a
2	NFYB	chr9:94878754-94878996	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:94853315..94855987-chr9:94878336..94879911,2	MCF-7	breast:
2	chr9:94859639..94862481-chr9:94877750..94879345,2	MCF-7	breast:
3	chr9:94867851..94872295-chr9:94876110..94878962,5	MCF-7	breast:
4	chr9:94875796..94880000-chr9:95086097..95090720,4	MCF-7	breast:
5	chr9:94876370..94880607-chr9:95003262..95006634,4	MCF-7	breast:
6	chr9:94871412..94875028-chr9:94875797..94879228,6	K562	blood:
7	chr9:94878737..94881456-chr9:95049160..95050675,2	K562	blood:

No data

Variant related genes	Relation type
SPTLC1	TF binding region
ENSG00000228069	Chromatin interaction
ENSG00000090054	Chromatin interaction
ENSG00000238288	Chromatin interaction
ENSG00000196305	Chromatin interaction
ENSG00000227321	Chromatin interaction
ENSG00000240791	Chromatin interaction
ENSG00000232179	Chromatin interaction
ENSG00000198000	Chromatin interaction
ENSG00000188312	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10115181	0.85[ASN][1000 genomes]
rs10115565	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10116088	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10117113	0.85[ASN][1000 genomes]
rs10117143	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10117394	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10118409	0.82[EUR][1000 genomes]
rs10118614	0.90[ASN][1000 genomes]
rs10118847	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119603	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10119983	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10121430	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10121694	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10121928	0.92[EUR][1000 genomes]
rs10122415	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10122798	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123181	0.90[ASN][1000 genomes]
rs10123678	0.85[ASN][1000 genomes]
rs10124473	0.90[ASN][1000 genomes]
rs10124705	0.92[EUR][1000 genomes]
rs10992194	0.88[EUR][1000 genomes]
rs10992202	0.96[EUR][1000 genomes]
rs10992223	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12336291	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12336497	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12336689	0.90[ASN][1000 genomes]
rs12338124	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12341602	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12341791	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12343645	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12343647	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12344414	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12345896	0.90[ASN][1000 genomes]
rs12347966	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348496	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12349001	0.92[EUR][1000 genomes]
rs12349327	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12352341	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12353142	0.85[ASN][1000 genomes]
rs12353321	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16908106	0.90[ASN][1000 genomes]
rs16908113	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16908131	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28391324	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28429191	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28437390	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28477960	0.92[EUR][1000 genomes]
rs28504279	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28505748	0.90[ASN][1000 genomes]
rs28513744	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28552704	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28637477	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28735483	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28744634	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28759240	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28804693	0.90[ASN][1000 genomes]
rs28819206	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28825409	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28883017	0.85[ASN][1000 genomes]
rs3858086	0.90[ASN][1000 genomes]
rs4302907	0.85[ASN][1000 genomes]
rs4344138	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4498616	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4560856	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4604504	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56204501	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56208357	0.90[ASN][1000 genomes]
rs56248784	0.90[ASN][1000 genomes]
rs56266486	0.92[EUR][1000 genomes]
rs57496363	0.92[EUR][1000 genomes]
rs57862149	0.92[EUR][1000 genomes]
rs58224960	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58679317	0.86[EUR][1000 genomes]
rs59790820	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60230478	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60743157	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61000917	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61246786	0.82[EUR][1000 genomes]
rs61456615	0.96[EUR][1000 genomes]
rs7018595	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7018827	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7021285	0.90[ASN][1000 genomes]
rs7021408	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7024215	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025703	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7027257	0.90[ASN][1000 genomes]
rs7028378	0.85[ASN][1000 genomes]
rs7033888	0.92[EUR][1000 genomes]
rs7034509	0.90[ASN][1000 genomes]
rs7035964	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7039366	0.85[ASN][1000 genomes]
rs7045602	0.84[EUR][1000 genomes]
rs7046206	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7047389	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73510406	0.85[ASN][1000 genomes]
rs73510411	0.90[ASN][1000 genomes]
rs73512337	0.90[ASN][1000 genomes]
rs73512339	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73512378	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73522907	0.92[EUR][1000 genomes]
rs73522929	0.92[EUR][1000 genomes]
rs73527329	0.85[ASN][1000 genomes]
rs73527330	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73653014	0.96[EUR][1000 genomes]
rs7848959	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7849664	0.85[ASN][1000 genomes]
rs7851412	0.92[EUR][1000 genomes]
rs7852989	0.85[ASN][1000 genomes]
rs7864340	0.85[ASN][1000 genomes]
rs7865994	0.90[ASN][1000 genomes]
rs7867659	0.92[EUR][1000 genomes]
rs7870339	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7870565	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7871565	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7871997	1.00[EUR][1000 genomes]
rs7872238	0.90[ASN][1000 genomes]
rs9696251	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61596207	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94878200-94885200	Weak transcription	Gastric	stomach
2	chr9:94878200-94896400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:94878400-94879000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr9:94878400-94880000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr9:94878400-94883400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:94878600-94879400	Enhancers	Primary B cells from cord blood	blood
7	chr9:94878600-94880000	Weak transcription	K562	blood
8	chr9:94878600-94880400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr9:94878600-94880400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr9:94878600-94880600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:94878800-94879000	Enhancers	Dnd41	blood

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