Variant report

Variant	rs17108815
Chromosome Location	chr14:39577348-39577349
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	chr14:39576417-39577386	A549	lung:	n/a	chr14:39576931-39576949 chr14:39576933-39576954 chr14:39576934-39576947 chr14:39576932-39576948
2	CTCF	chr14:39577220-39577370	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:39571044..39574449-chr14:39575206..39581914,9	K562	blood:
2	chr14:39576813..39577373-chr14:39841108..39841759,2	MCF-7	breast:
3	chr14:39569997..39574883-chr14:39575393..39578347,7	MCF-7	breast:
4	chr14:39572308..39574521-chr14:39576459..39578520,2	MCF-7	breast:
5	chr14:39576976..39580513-chr14:39638047..39641153,4	K562	blood:
6	chr14:39570753..39574803-chr14:39575206..39579488,6	K562	blood:

Variant related genes	Relation type
SEC23A	TF binding region
ENSG00000258591	TF binding region
ENSG00000100934	Chromatin interaction
ENSG00000182400	Chromatin interaction
ENSG00000258651	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs45469295	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs45469795	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45540035	0.90[EUR][1000 genomes]
rs55790340	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55880223	0.83[EUR][1000 genomes]
rs55918207	0.81[EUR][1000 genomes]
rs55981737	0.83[EUR][1000 genomes]
rs55997577	0.90[EUR][1000 genomes]
rs56032918	0.83[EUR][1000 genomes]
rs56063785	0.81[EUR][1000 genomes]
rs56074634	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56087094	0.81[EUR][1000 genomes]
rs56103446	0.90[EUR][1000 genomes]
rs56125789	0.90[EUR][1000 genomes]
rs56136756	0.81[EUR][1000 genomes]
rs56225465	0.85[EUR][1000 genomes]
rs56237815	0.81[EUR][1000 genomes]
rs56282196	0.83[EUR][1000 genomes]
rs56328886	0.81[EUR][1000 genomes]
rs56333870	0.87[EUR][1000 genomes]
rs56334607	0.81[EUR][1000 genomes]
rs56335002	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56341545	0.81[EUR][1000 genomes]
rs56404404	0.83[EUR][1000 genomes]
rs57248532	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59418195	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6571906	0.89[CEU][hapmap]
rs6571907	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs67808375	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7147914	0.83[EUR][1000 genomes]
rs7148908	0.96[EUR][1000 genomes]
rs7150638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72669388	0.81[EUR][1000 genomes]
rs72669397	0.81[EUR][1000 genomes]
rs72671316	0.81[EUR][1000 genomes]
rs72671333	0.81[EUR][1000 genomes]
rs72671344	0.81[EUR][1000 genomes]
rs72671349	0.81[EUR][1000 genomes]
rs72671353	0.81[EUR][1000 genomes]
rs72671360	0.85[EUR][1000 genomes]
rs72671362	0.85[EUR][1000 genomes]
rs72671367	0.85[EUR][1000 genomes]
rs72671372	0.90[EUR][1000 genomes]
rs72671379	0.90[EUR][1000 genomes]
rs72671382	0.90[EUR][1000 genomes]
rs72671387	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs72671398	0.90[EUR][1000 genomes]
rs72671400	0.90[EUR][1000 genomes]
rs72673307	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs72673314	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72673315	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72673316	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673317	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673318	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673328	0.88[EUR][1000 genomes]
rs72673329	0.88[EUR][1000 genomes]
rs72673339	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72673340	0.81[EUR][1000 genomes]
rs72673346	0.83[EUR][1000 genomes]
rs72673350	0.83[EUR][1000 genomes]
rs72673357	0.81[EUR][1000 genomes]
rs8009457	0.81[EUR][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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv983817	chr14:39577051-39579335	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17108815	TRAPPC6B	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39573200-39577800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:39573400-39578800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr14:39573400-39579000	Weak transcription	K562	blood
4	chr14:39573400-39582400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:39573400-39583000	Weak transcription	HSMM	muscle
6	chr14:39573800-39583000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr14:39573800-39583000	Weak transcription	Thymus	Thymus
8	chr14:39574000-39582400	Weak transcription	A549	lung
9	chr14:39574000-39582800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr14:39574000-39583000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr14:39574000-39583000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr14:39574000-39583000	Weak transcription	Stomach Mucosa	stomach
13	chr14:39574200-39582400	Weak transcription	Dnd41	blood
14	chr14:39574200-39583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr14:39574400-39578400	Weak transcription	GM12878-XiMat	blood
16	chr14:39574400-39582400	Weak transcription	Hela-S3	cervix
17	chr14:39574400-39582800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr14:39576400-39578000	Enhancers	HepG2	liver
19	chr14:39576800-39577600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr14:39577200-39582400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr14:39577200-39582800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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