Variant report

Variant	rs1075845
Chromosome Location	chr15:83350617-83350618
allele	C/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:16)
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	CEBPB	chr15:83350322-83350774	MCF-7	breast:	n/a	chr15:83350536-83350549
2	STAT3	chr15:83350496-83350670	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83349249..83350821-chr15:83733828..83735921,2	K562	blood:
2	chr15:83315715..83320562-chr15:83347753..83351536,6	K562	blood:
3	chr15:83316633..83319257-chr15:83348234..83350901,2	MCF-7	breast:
4	chr15:83347963..83350756-chr15:83406519..83408532,2	K562	blood:
5	chr15:83313759..83319278-chr15:83347483..83351536,8	K562	blood:
6	chr15:83348934..83350853-chr15:83378356..83380655,2	K562	blood:
7	chr15:83346733..83351654-chr15:83416978..83420559,7	MCF-7	breast:
8	chr15:83349235..83351553-chr15:83406587..83408989,2	MCF-7	breast:
9	chr15:83348154..83351401-chr15:83364138..83368453,6	MCF-7	breast:
10	chr15:83348285..83351278-chr15:83678934..83682211,3	MCF-7	breast:
11	chr15:83348193..83350766-chr15:83477443..83480779,4	MCF-7	breast:
12	chr15:83294774..83297381-chr15:83349087..83350883,2	MCF-7	breast:
13	chr15:83347977..83352145-chr15:83417264..83422141,9	MCF-7	breast:
14	chr15:83348209..83350926-chr15:83376211..83377868,2	MCF-7	breast:
15	chr15:83347908..83350889-chr3:44378735..44380988,2	MCF-7	breast:
16	chr15:83330561..83333118-chr15:83349292..83351934,2	K562	blood:

No data

Variant related genes	Relation type
AP3B2	TF binding region
ENSG00000252690	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000271937	Chromatin interaction
ENSG00000259315	Chromatin interaction
ENSG00000064726	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000103723	Chromatin interaction
ENSG00000250988	Chromatin interaction
ENSG00000260608	Chromatin interaction
ENSG00000259462	Chromatin interaction
ENSG00000179152	Chromatin interaction
ENSG00000214575	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17158366	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.98[ASN][1000 genomes]
rs17841169	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17841176	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs1864700	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs55870914	0.98[ASN][1000 genomes]
rs57154772	0.81[ASN][1000 genomes]
rs57217657	0.87[ASN][1000 genomes]
rs57578325	0.95[ASN][1000 genomes]
rs60160189	0.87[ASN][1000 genomes]
rs60451143	0.98[ASN][1000 genomes]
rs66793760	0.97[ASN][1000 genomes]
rs67205493	0.98[ASN][1000 genomes]
rs73439163	0.96[ASN][1000 genomes]
rs7495972	0.97[ASN][1000 genomes]
rs8028363	0.85[ASN][1000 genomes]
rs8032281	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8036227	0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	esv1808975	chr15:83307574-83360168	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	esv3443566	chr15:83346946-83367664	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv904450	chr15:83347193-83395340	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1075845	HDGFRP3	cis	lymphoblastoid	seeQTL
rs1075845	GOLGA6L9	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83346400-83357400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:83346600-83357200	Weak transcription	Brain Angular Gyrus	brain
3	chr15:83347800-83357000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:83349800-83356600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:83349800-83377200	Weak transcription	Brain Anterior Caudate	brain
6	chr15:83350400-83357200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:83350400-83368000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:83350400-83369800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:83350400-83372800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:83350600-83356000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:83350600-83357200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:83350600-83368400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:83350600-83369000	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links