Variant report

Variant	rs8036962
Chromosome Location	chr15:99641470-99641471
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	chr15:99640181-99641773	A549	lung:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953

No.	Distal block	Cell Line	Cell type
1	chr15:99640023..99641527-chr15:99752943..99754403,15	MCF-7	breast:
2	chr15:99640493..99643372-chr15:99648105..99650704,2	MCF-7	breast:
3	chr15:99640426..99641482-chr15:99753072..99754322,8	K562	blood:
4	chr15:99634162..99637138-chr15:99639706..99641886,2	MCF-7	breast:
5	chr15:99639780..99642328-chr15:99644918..99646902,2	MCF-7	breast:
6	chr15:99639243..99641590-chr15:99753533..99755577,2	MCF-7	breast:

Variant related genes	Relation type
SYNM	TF binding region
ENSG00000182253	Chromatin interaction
ENSG00000259475	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11014	0.81[EUR][1000 genomes]
rs11636944	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12439693	0.83[MEX][hapmap]
rs12440758	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12440983	0.96[ASN][1000 genomes]
rs166332	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1670267	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1670268	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1703796	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1703797	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2312484	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs260097	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.96[ASN][1000 genomes]
rs260098	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260100	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260111	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs260112	0.83[MEX][hapmap]
rs35049808	0.96[ASN][1000 genomes]
rs6598223	0.96[ASN][1000 genomes]
rs7496161	0.84[CHD][hapmap]
rs8028199	0.83[ASN][1000 genomes]
rs8028233	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8033198	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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 target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv904544	chr15:99524865-99655744	Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
15	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
17	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8036962	DMN	cis	multi-tissue	Pritchard
rs8036962	TTC23	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99640800-99645000	Weak transcription	Pancreas	Pancrea
2	chr15:99641000-99641800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:99641000-99642400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:99641000-99642400	Weak transcription	Psoas Muscle	Psoas
5	chr15:99641000-99644800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:99641000-99645000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:99641000-99645000	Weak transcription	Right Ventricle	heart
8	chr15:99641000-99645200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:99641000-99645200	Weak transcription	Gastric	stomach
10	chr15:99641200-99641600	Enhancers	A549	lung
11	chr15:99641200-99642000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:99641200-99644800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:99641200-99644800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:99641200-99645200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:99641200-99645200	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:99641200-99645400	Weak transcription	Brain Substantia Nigra	brain
17	chr15:99641400-99641800	Weak transcription	Adipose Nuclei	Adipose

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