Variant report

Variant	rs17862866
Chromosome Location	chr2:234610912-234610913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234609669..234612575-chr2:234763308..234766192,2	MCF-7	breast:
2	chr2:234604730..234606945-chr2:234609647..234612272,2	K562	blood:
3	chr2:234610804..234613588-chr2:234613696..234615763,4	MCF-7	breast:
4	chr2:234393470..234398510-chr2:234607909..234611299,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10179091	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs10929301	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1104892	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11685892	0.84[ASN][1000 genomes]
rs2008595	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs2012734	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2221198	0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs2363116	0.85[ASN][1000 genomes]
rs3755319	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs3806596	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806597	0.86[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap]
rs3821242	0.80[ASN][1000 genomes]
rs4124874	0.85[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4148326	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs4233633	0.86[CHB][hapmap]
rs4294999	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs4399719	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4467260	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4521035	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4663325	0.86[CHB][hapmap]
rs4663327	0.86[CHB][hapmap]
rs4663333	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4663963	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs4663965	0.85[CEU][hapmap];0.93[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs4663967	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4663969	0.82[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs4663971	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6431628	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6706232	0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6711351	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6715325	0.93[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs6741669	0.85[CEU][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6760025	1.00[YRI][hapmap]
rs7556676	0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs7572563	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574296	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7597496	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs871514	0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats 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	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17862866	DGKD	cis	cerebellum	SCAN
rs17862866	ARL4C	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234602800-234614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:234609000-234611000	Weak transcription	Liver	Liver
3	chr2:234609000-234611000	Weak transcription	HUVEC	blood vessel
4	chr2:234609000-234614400	Weak transcription	Stomach Mucosa	stomach
5	chr2:234609000-234614800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:234609200-234611400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:234609200-234614000	Weak transcription	NHEK	skin
8	chr2:234609200-234614200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:234610600-234611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:234610800-234611600	Enhancers	Hela-S3	cervix
11	chr2:234610800-234612200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:234610800-234613200	ZNF genes & repeats	A549	lung

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