Variant report

Variant	rs6505173
Chromosome Location	chr17:28646057-28646058
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	chr17:28637592..28639330-chr17:28645800..28647531,2	MCF-7	breast:
2	chr17:28443598..28445431-chr17:28645496..28648221,2	K562	blood:

Variant related genes	Relation type
ENSG00000126653	Chromatin interaction
ENSG00000265394	Chromatin interaction
ENSG00000199071	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1050565	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs11656408	0.82[EUR][1000 genomes]
rs11867581	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12939390	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs12949747	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs13341611	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1487971	0.84[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17767256	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs2321705	0.88[ASN][1000 genomes]
rs3103305	0.89[ASN][1000 genomes]
rs3110094	0.86[ASN][1000 genomes]
rs3110095	0.86[ASN][1000 genomes]
rs3110452	0.94[JPT][hapmap]
rs3110453	0.89[ASN][1000 genomes]
rs33980254	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3764449	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3794806	0.94[JPT][hapmap]
rs3816828	0.85[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505165	0.85[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505169	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6505171	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7208052	0.94[JPT][hapmap]
rs7210085	0.85[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7214014	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7214248	0.94[JPT][hapmap]
rs7214991	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7215330	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7223821	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7342921	0.94[JPT][hapmap]
rs7342929	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8072345	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8073378	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8080300	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9896548	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064975	chr17:28604187-28851905	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers 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	37 gene(s)	inside rSNPs	diseases
2	nsv543299	chr17:28604187-28851905	Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv543300	chr17:28620420-28659310	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6505173	SARM1	cis	cerebellum	SCAN
rs6505173	GOSR1	cis	parietal	SCAN
rs6505173	SUZ12P	cis	parietal	SCAN
rs6505173	GIT1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:28639800-28653800	Weak transcription	Fetal Intestine Large	intestine
2	chr17:28642400-28647800	Weak transcription	HepG2	liver
3	chr17:28643600-28648400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:28644000-28667000	Weak transcription	Colonic Mucosa	Colon
5	chr17:28644200-28672600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:28644400-28658400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:28645000-28646400	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr17:28645600-28650400	Weak transcription	K562	blood
9	chr17:28645600-28653800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr17:28645800-28648200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:28645800-28649200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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