Variant report

Variant	rs17260529
Chromosome Location	chr1:210711094-210711095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10779535	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs10779536	0.87[EUR][1000 genomes]
rs10779537	0.87[EUR][1000 genomes]
rs11119530	0.94[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119534	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119537	0.84[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs11583167	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584633	1.00[ASN][1000 genomes]
rs11585911	1.00[ASN][1000 genomes]
rs12033957	0.87[EUR][1000 genomes]
rs12121595	0.87[EUR][1000 genomes]
rs12121717	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122405	0.87[EUR][1000 genomes]
rs12122988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125970	0.87[EUR][1000 genomes]
rs12126012	0.87[EUR][1000 genomes]
rs12126287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127170	0.87[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129347	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129382	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132714	0.84[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12136151	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343876	1.00[ASN][1000 genomes]
rs17188337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17260445	1.00[CHD][hapmap]
rs17260515	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17260522	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892471	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892472	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069151	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs4540660	0.83[EUR][1000 genomes]
rs4845044	0.84[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4845045	0.84[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs56727567	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58599805	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59289142	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59525134	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60629769	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828096	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828129	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828131	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828132	1.00[ASN][1000 genomes]
rs6540602	1.00[CHD][hapmap]
rs6659137	1.00[ASN][1000 genomes]
rs6680553	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685262	1.00[ASN][1000 genomes]
rs72749373	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534803	1.00[CHD][hapmap]
rs7551813	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv549106	chr1:210698719-210736508	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1011702	chr1:210706323-210739030	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv988198	chr1:210707300-210716552	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17260529	LGTN	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210674400-210719600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:210680600-210731000	Weak transcription	HSMM	muscle
3	chr1:210709400-210715200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:210709800-210715200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:210710000-210715000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:210710000-210715000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:210710000-210715000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:210710000-210715200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:210710000-210715200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:210710000-210715400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:210710200-210715200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:210710200-210715200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:210710200-210715200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:210710400-210715200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:210710600-210715200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:210710800-210719000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:210711000-210715000	Weak transcription	HSMMtube	muscle

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