Variant report

Variant	rs4653509
Chromosome Location	chr1:227698733-227698734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227696113..227699015-chr1:227705081..227707461,4	K562	blood:
2	chr1:227696655..227700997-chr1:227705079..227707461,4	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10495277	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799429	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799438	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs1080061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916172	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10916177	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1154835	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs11805477	0.84[CEU][hapmap]
rs11806830	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs11807529	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12120313	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12122398	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12126339	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12131517	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12133008	0.81[ASN][1000 genomes]
rs12135976	0.81[ASN][1000 genomes]
rs12137033	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12138942	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs12408514	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1390400	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16847875	0.81[YRI][hapmap]
rs1874371	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1923822	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1951729	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2012386	0.81[ASN][1000 genomes]
rs2088213	0.83[YRI][hapmap]
rs2093608	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2313245	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2999750	0.82[AMR][1000 genomes]
rs3010188	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4306097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653851	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653862	0.81[ASN][1000 genomes]
rs4653864	0.80[ASN][1000 genomes]
rs55721361	0.81[ASN][1000 genomes]
rs56349581	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58274339	0.81[ASN][1000 genomes]
rs6426469	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs6667937	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6699448	0.81[ASN][1000 genomes]

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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv945337	chr1:227680551-227712483	ZNF genes & repeats Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4653509	ZNF678	cis	lesional skin	skin_eQTL
rs4653509	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs4653509	ZNF678	cis	normal skin	skin_eQTL
rs4653509	ZNF678	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227696600-227699600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links