Variant report

Variant	rs712862
Chromosome Location	chr1:223385795-223385796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223304714..223306569-chr1:223385509..223387660,2	MCF-7	breast:
2	chr1:223315506..223317996-chr1:223384708..223386864,2	MCF-7	breast:
3	chr1:223384376..223385879-chr1:223415413..223417921,2	MCF-7	breast:
4	chr1:223382567..223385980-chr1:223405719..223408418,3	K562	blood:
5	chr1:222815490..222817293-chr1:223385380..223388069,2	K562	blood:

Variant related genes	Relation type
ENSG00000236846	Chromatin interaction
ENSG00000187554	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11485986	0.98[ASN][1000 genomes]
rs11485987	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs11485988	0.87[EUR][1000 genomes]
rs11488551	0.87[EUR][1000 genomes]
rs1612521	0.91[ASN][1000 genomes]
rs1640803	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1640811	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1640812	0.86[JPT][hapmap]
rs1640813	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1640816	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1773719	0.91[ASN][1000 genomes]
rs1773722	0.91[ASN][1000 genomes]
rs1773723	0.91[ASN][1000 genomes]
rs1773753	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1935305	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2160152	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2430407	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2430408	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2430409	0.86[EUR][1000 genomes]
rs2430410	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3121256	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34071437	0.86[EUR][1000 genomes]
rs34218350	0.86[EUR][1000 genomes]
rs35169648	0.87[EUR][1000 genomes]
rs35227692	0.86[EUR][1000 genomes]
rs35551279	0.86[EUR][1000 genomes]
rs35644560	0.87[EUR][1000 genomes]
rs35778136	0.86[EUR][1000 genomes]
rs35797130	0.91[ASN][1000 genomes]
rs3768284	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4661283	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4661284	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5744122	1.00[CEU][hapmap]
rs5744135	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs5744138	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs5744139	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs5744140	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs5744143	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs5744149	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs712863	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712865	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725972	0.91[ASN][1000 genomes]
rs73118176	0.87[EUR][1000 genomes]
rs73118177	0.87[EUR][1000 genomes]
rs73118181	0.87[EUR][1000 genomes]
rs73118186	0.87[EUR][1000 genomes]
rs73118187	0.87[EUR][1000 genomes]
rs73118190	0.87[EUR][1000 genomes]
rs73118193	0.87[EUR][1000 genomes]
rs73118194	0.87[EUR][1000 genomes]
rs73118198	0.87[EUR][1000 genomes]
rs73118201	0.87[EUR][1000 genomes]
rs73118202	0.87[EUR][1000 genomes]
rs73120203	0.87[EUR][1000 genomes]
rs73120204	0.87[EUR][1000 genomes]
rs73120207	0.87[EUR][1000 genomes]
rs73120219	0.87[EUR][1000 genomes]
rs73120224	0.87[EUR][1000 genomes]
rs73120229	0.87[EUR][1000 genomes]
rs73120232	0.87[EUR][1000 genomes]
rs73120236	0.86[EUR][1000 genomes]
rs73120250	0.86[EUR][1000 genomes]
rs73120253	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73120257	0.86[EUR][1000 genomes]
rs73120261	0.86[EUR][1000 genomes]
rs73120265	0.86[EUR][1000 genomes]
rs73120267	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120269	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120297	0.86[EUR][1000 genomes]
rs851140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs851144	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs851145	0.86[EUR][1000 genomes]
rs851146	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs851147	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs851148	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs851150	0.86[EUR][1000 genomes]
rs851151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs851152	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs851153	1.00[CEU][hapmap]
rs851154	0.86[EUR][1000 genomes]
rs851155	0.86[EUR][1000 genomes]
rs851156	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs851158	0.86[EUR][1000 genomes]
rs851160	1.00[ASN][1000 genomes]
rs851163	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851211	1.00[GIH][hapmap];0.85[JPT][hapmap]
rs851215	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs860372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs988241	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs988242	1.00[CHD][hapmap];0.86[JPT][hapmap]

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	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223371200-223389800	Weak transcription	Gastric	stomach
2	chr1:223377000-223392200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:223379600-223388000	Enhancers	Fetal Muscle Leg	muscle
4	chr1:223381400-223389400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:223383600-223386400	Enhancers	HSMMtube	muscle
6	chr1:223384000-223386200	Enhancers	Ovary	ovary
7	chr1:223384400-223386000	Enhancers	HSMM	muscle
8	chr1:223384800-223386200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:223385200-223386000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:223385200-223386200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:223385600-223386600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:223385600-223387000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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