Variant report

Variant	rs41405647
Chromosome Location	chr15:34503327-34503328
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	CTCF	chr15:34503240-34503390	GM12870	blood:	n/a	n/a
2	ZNF143	chr15:34503298-34503328	Hela-S3	cervix:	n/a	n/a
3	CCNT2	chr15:34503248-34503580	K562	blood:	n/a	n/a
4	SMC3	chr15:34501507-34503372	SK-N-SH	brain:	n/a	chr15:34502391-34502405 chr15:34502391-34502401 chr15:34502063-34502073 chr15:34502541-34502549 chr15:34502398-34502405 chr15:34501929-34501939

No.	Distal block	Cell Line	Cell type
1	chr15:34499795..34503886-chr15:34627014..34631557,6	K562	blood:
2	chr15:34500839..34504564-chr15:34529168..34532268,3	K562	blood:
3	chr15:34500871..34503422-chr15:34659158..34662481,4	K562	blood:
4	chr15:34498121..34503791-chr15:34514506..34519551,14	K562	blood:
5	chr15:34391225..34395745-chr15:34498845..34504196,8	K562	blood:
6	chr15:34330950..34333091-chr15:34501411..34503652,2	K562	blood:
7	chr15:34502586..34504102-chr15:34521539..34524042,2	K562	blood:
8	chr15:34497680..34504001-chr15:34514973..34521212,14	K562	blood:
9	chr15:34500616..34503501-chr15:34610779..34612770,2	K562	blood:
10	chr15:34491377..34494902-chr15:34500682..34503965,3	K562	blood:

Variant related genes	Relation type
KATNBL1	TF binding region
ENSG00000182405	Chromatin interaction
ENSG00000169857	Chromatin interaction
ENSG00000176454	Chromatin interaction
ENSG00000134152	Chromatin interaction
ENSG00000134153	Chromatin interaction
ENSG00000128463	Chromatin interaction
ENSG00000140199	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10152261	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852315	0.88[ASN][1000 genomes]
rs11853345	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11853347	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11854298	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11856753	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11857604	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11857608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11858527	0.88[ASN][1000 genomes]
rs17236749	1.00[CHB][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs17554484	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817770	1.00[CHB][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs2118159	0.88[ASN][1000 genomes]
rs2118160	0.88[ASN][1000 genomes]
rs28406544	0.88[ASN][1000 genomes]
rs3764236	1.00[CHB][hapmap];0.86[GIH][hapmap];0.88[ASN][1000 genomes]
rs3829483	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486849	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4581678	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs55801303	0.88[ASN][1000 genomes]
rs6495624	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161944	1.00[CHB][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs7168139	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7176526	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7179249	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7183568	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73382081	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73382086	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73384011	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7497666	0.83[ASN][1000 genomes]
rs8037674	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672345	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672434	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672496	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672544	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9672784	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9806468	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41405647	HERC2	cis	parietal	SCAN
rs41405647	C15orf29	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34502400-34503800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr15:34502400-34504400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:34502400-34504600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:34502400-34504600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:34502400-34504600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:34502400-34504600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:34502400-34504600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:34502600-34504400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:34502600-34506200	Weak transcription	Fetal Thymus	thymus
10	chr15:34502600-34510000	Weak transcription	NHLF	lung
11	chr15:34502800-34503400	Enhancers	HepG2	liver
12	chr15:34502800-34504600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:34503000-34503600	Enhancers	K562	blood
14	chr15:34503200-34504600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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