Variant report

Variant	rs7864609
Chromosome Location	chr9:117884216-117884217
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	NFIC	chr9:117883098-117884247	ECC-1	luminal epithelium:	n/a	chr9:117883561-117883578
2	TCF12	chr9:117883029-117884239	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr9:117883228-117884348	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10119915	1.00[JPT][hapmap]
rs10120799	1.00[JPT][hapmap]
rs10122188	1.00[JPT][hapmap]
rs10125919	1.00[JPT][hapmap]
rs10465131	0.93[ASN][1000 genomes]
rs10817719	1.00[JPT][hapmap]
rs10817720	1.00[JPT][hapmap]
rs10817726	1.00[JPT][hapmap]
rs10982548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10982549	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10982551	0.93[ASN][1000 genomes]
rs10982560	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982563	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982564	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982565	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982566	0.95[ASN][1000 genomes]
rs10982568	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982569	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982570	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982571	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982573	0.95[ASN][1000 genomes]
rs10982574	0.95[ASN][1000 genomes]
rs10982575	0.95[ASN][1000 genomes]
rs10982580	0.95[ASN][1000 genomes]
rs10982581	0.95[ASN][1000 genomes]
rs10982582	0.95[ASN][1000 genomes]
rs10982583	0.93[ASN][1000 genomes]
rs10982584	0.95[ASN][1000 genomes]
rs10982585	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982586	0.95[ASN][1000 genomes]
rs10982588	0.95[ASN][1000 genomes]
rs10982589	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10982590	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10982591	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10982597	1.00[JPT][hapmap]
rs10982610	1.00[JPT][hapmap]
rs12235377	1.00[JPT][hapmap]
rs12237691	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12338815	0.95[ASN][1000 genomes]
rs12338911	0.95[ASN][1000 genomes]
rs12347993	0.95[ASN][1000 genomes]
rs12348952	0.95[ASN][1000 genomes]
rs1335331	0.94[MKK][hapmap]
rs16932289	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16932349	1.00[JPT][hapmap]
rs56791225	0.93[ASN][1000 genomes]
rs59205962	0.90[ASN][1000 genomes]
rs60003319	0.90[ASN][1000 genomes]
rs60760004	0.93[ASN][1000 genomes]
rs6478135	1.00[CEU][hapmap]
rs6478136	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6478138	0.95[ASN][1000 genomes]
rs6478139	0.95[ASN][1000 genomes]
rs6478140	0.95[ASN][1000 genomes]
rs6478141	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6478142	0.95[ASN][1000 genomes]
rs6478144	0.95[ASN][1000 genomes]
rs7027235	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7027851	0.93[ASN][1000 genomes]
rs7029796	0.82[AFR][1000 genomes]
rs7031730	0.95[ASN][1000 genomes]
rs7033388	0.94[MKK][hapmap]
rs7847093	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7851019	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7851086	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7851110	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7851481	0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7859387	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7862558	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9886855	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7864609	MAP1B	trans	brain	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117881400-117884400	Enhancers	NH-A	brain
2	chr9:117881400-117886000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr9:117881600-117884400	Enhancers	NHEK	skin
4	chr9:117881800-117884400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr9:117882000-117888800	Weak transcription	NHLF	lung
6	chr9:117882400-117884400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:117882600-117885400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:117882800-117884400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:117883200-117884400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:117883200-117884400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:117883200-117884400	Enhancers	HMEC	breast
12	chr9:117883400-117884400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:117883600-117888600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:117884000-117884400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:117884000-117887200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:117884000-117888800	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:117884000-117892600	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:117884200-117888800	Weak transcription	Osteobl	bone

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