Variant report

Variant	rs41315860
Chromosome Location	chr1:247375860-247375861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr1:247375133-247376192	GM12878	blood:	n/a	n/a
2	EP300	chr1:247375146-247375888	GM12878	blood:	n/a	chr1:247375331-247375345
3	CHD2	chr1:247374928-247375920	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr1:247375250-247375970	GM12878	blood:	n/a	n/a
5	TEAD4	chr1:247375299-247375881	K562	blood:	n/a	n/a
6	TEAD4	chr1:247375372-247375869	K562	blood:	n/a	n/a
7	EP300	chr1:247375455-247375940	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:247375650..247377516-chr1:247377910..247380248,2	K562	blood:
2	chr1:247374235..247377046-chr1:247498080..247500631,2	K562	blood:
3	chr1:247274493..247276812-chr1:247371838..247375899,3	K562	blood:
4	chr1:247375724..247377747-chr1:247379466..247381857,2	K562	blood:

Variant related genes	Relation type
MIR3916	TF binding region
ENSG00000221953	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10924964	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1115202	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12567626	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12569042	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17269923	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2380117	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2892054	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35229190	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3738443	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4269806	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351686	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4551629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4582838	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55643126	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55914345	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56029850	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56046175	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56065612	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56340510	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58405512	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60240280	0.84[EUR][1000 genomes]
rs60698393	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61839991	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61839994	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61839996	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61839997	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61840000	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61840048	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61840053	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61840054	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61840055	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61840056	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61840057	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61840059	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6656425	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6660351	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6665647	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6666543	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668154	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6680197	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6684181	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6698690	0.88[EUR][1000 genomes]
rs74152976	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7536883	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7546908	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7551871	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
6	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
8	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
9	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41315860	RP11-488L18.10	cis	Artery Tibial	GTEx
rs41315860	RP11-488L18.10	cis	lung	GTEx
rs41315860	RP11-488L18.10	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247374200-247379600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:247374600-247376200	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:247374600-247376200	Flanking Active TSS	GM12878-XiMat	blood
4	chr1:247374600-247376800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:247374600-247376800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr1:247374600-247377200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:247374600-247377200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr1:247374600-247377200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:247374600-247379600	Weak transcription	Fetal Thymus	thymus
10	chr1:247374800-247377000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr1:247375000-247376000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:247375000-247376400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:247375000-247377200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:247375200-247376600	Enhancers	HepG2	liver
15	chr1:247375400-247376200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:247375400-247376200	Enhancers	HSMM	muscle
17	chr1:247375600-247376400	Weak transcription	NHDF-Ad	bronchial
18	chr1:247375600-247376600	Enhancers	K562	blood
19	chr1:247375600-247377200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:247375800-247376800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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