Variant report

Variant	rs3850554
Chromosome Location	chr1:57868438-57868439
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10159302	0.82[GIH][hapmap];1.00[ASN][1000 genomes]
rs10493218	0.89[ASW][hapmap];0.80[CEU][hapmap];0.94[GIH][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800574	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803541	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807631	0.80[CEU][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424471	0.82[GIH][hapmap];1.00[ASN][1000 genomes]
rs1424472	1.00[ASN][1000 genomes]
rs17096836	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115683	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115722	1.00[ASW][hapmap];0.80[CEU][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115739	1.00[ASW][hapmap];0.80[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17115757	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115767	0.80[CEU][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778031	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17838097	0.80[ASW][hapmap];0.90[CEU][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981891	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35664891	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738552	1.00[ASW][hapmap];0.80[CEU][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850553	1.00[ASW][hapmap];0.80[CEU][hapmap];0.94[GIH][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4309005	1.00[ASN][1000 genomes]
rs4912242	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912245	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs507466	0.80[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524941	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60790797	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657926	1.00[ASN][1000 genomes]
rs72909225	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909227	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909233	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909243	1.00[ASN][1000 genomes]
rs72909245	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541150	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541309	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57858000-57868600	Weak transcription	Fetal Brain Male	brain
2	chr1:57860400-57874600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:57862400-57870800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:57862400-57873200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:57863800-57875400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:57864400-57873400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:57866600-57870600	Weak transcription	Stomach Mucosa	stomach
8	chr1:57867400-57872800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:57867600-57874400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:57867800-57870400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:57867800-57874600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:57867800-57875400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:57868000-57873600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:57868200-57870000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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