Variant report

Variant	rs9901294
Chromosome Location	chr17:19888501-19888502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19881237..19883350-chr17:19887279..19889382,2	K562	blood:
2	chr17:19880420..19882737-chr17:19888163..19890005,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11204422	0.89[JPT][hapmap]
rs11867585	0.81[JPT][hapmap]
rs11870381	0.90[JPT][hapmap]
rs12449662	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12450857	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12451841	0.90[JPT][hapmap]
rs12453720	0.95[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12936794	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12942179	0.81[JPT][hapmap]
rs12943369	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12944084	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12947713	0.90[JPT][hapmap]
rs1638526	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1638527	0.87[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1638528	0.95[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs169413	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17604987	0.87[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17605101	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17668529	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17686798	0.90[JPT][hapmap]
rs17759609	0.87[CEU][hapmap];0.87[MEX][hapmap]
rs17759959	0.90[JPT][hapmap]
rs203449	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs203454	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs203464	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs203467	0.87[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs203474	0.86[EUR][1000 genomes]
rs203475	0.87[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs203476	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs203478	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs203480	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2072337	1.00[JPT][hapmap]
rs2108981	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28424266	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34182788	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34726000	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35254155	0.83[AMR][1000 genomes]
rs35315252	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35925051	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35979784	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36097967	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs403021	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4141185	1.00[JPT][hapmap]
rs427033	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4924808	0.90[JPT][hapmap]
rs4925063	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4925064	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4925075	0.90[JPT][hapmap];0.83[MEX][hapmap]
rs4925082	0.90[JPT][hapmap]
rs56005410	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62066345	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066346	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066347	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62066348	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066349	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066350	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066351	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066352	0.84[AMR][1000 genomes]
rs6587207	0.90[JPT][hapmap]
rs6813	0.94[ASW][hapmap];0.91[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7207459	0.90[JPT][hapmap]
rs7209653	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215803	0.90[JPT][hapmap]
rs7224875	0.90[JPT][hapmap]
rs8065122	0.82[ASN][1000 genomes]
rs8068484	0.90[JPT][hapmap]
rs8075343	0.90[JPT][hapmap]
rs8079923	0.87[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8080190	0.90[JPT][hapmap]
rs850622	0.87[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs888424	0.90[JPT][hapmap]
rs9891503	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9893296	0.86[ASN][1000 genomes]
rs9897653	0.81[JPT][hapmap]
rs9915039	0.90[JPT][hapmap]
rs9944451	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9901294	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs9901294	AKAP10	cis	Lymphoblastoid	GTEx
rs9901294	AKAP10	cis	lymphoblastoid	seeQTL
rs9901294	SMCR5	cis	parietal	SCAN
rs9901294	AKAP10	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19883800-19890800	Weak transcription	Right Atrium	heart
2	chr17:19884200-19890000	Weak transcription	Placenta	Placenta
3	chr17:19884400-19890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:19888400-19888800	Enhancers	Fetal Heart	heart

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