Variant report

Variant	rs2430408
Chromosome Location	chr1:223389870-223389871
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	chr1:223388784..223390736-chr1:223399885..223401749,2	MCF-7	breast:
2	chr1:223386685..223389048-chr1:223389163..223390831,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11485986	0.98[ASN][1000 genomes]
rs11485987	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs1612521	0.95[ASN][1000 genomes]
rs1640803	1.00[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs1640811	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1640812	0.86[JPT][hapmap]
rs1640813	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1640816	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1773719	0.95[ASN][1000 genomes]
rs1773722	0.95[ASN][1000 genomes]
rs1773723	0.95[ASN][1000 genomes]
rs1773753	0.83[AMR][1000 genomes]
rs1935305	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs2160152	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2430407	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430409	1.00[EUR][1000 genomes]
rs2430410	0.95[ASN][1000 genomes]
rs3121256	0.95[ASN][1000 genomes]
rs34071437	1.00[EUR][1000 genomes]
rs34218350	1.00[EUR][1000 genomes]
rs35227692	1.00[EUR][1000 genomes]
rs35412940	0.86[EUR][1000 genomes]
rs35551279	1.00[EUR][1000 genomes]
rs35778136	1.00[EUR][1000 genomes]
rs35797130	0.95[ASN][1000 genomes]
rs3768284	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4661283	0.95[ASN][1000 genomes]
rs4661284	0.95[ASN][1000 genomes]
rs5744122	1.00[CEU][hapmap]
rs5744135	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs5744138	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs5744139	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs5744140	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs5744143	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs5744149	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs712862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712863	0.95[ASN][1000 genomes]
rs712865	0.95[ASN][1000 genomes]
rs725972	0.95[ASN][1000 genomes]
rs73118166	0.86[EUR][1000 genomes]
rs73118168	0.86[EUR][1000 genomes]
rs73118170	0.86[EUR][1000 genomes]
rs73118175	0.86[EUR][1000 genomes]
rs73120206	0.86[EUR][1000 genomes]
rs73120222	0.86[EUR][1000 genomes]
rs73120234	0.86[EUR][1000 genomes]
rs73120236	1.00[EUR][1000 genomes]
rs73120250	1.00[EUR][1000 genomes]
rs73120253	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73120257	1.00[EUR][1000 genomes]
rs73120261	1.00[EUR][1000 genomes]
rs73120265	1.00[EUR][1000 genomes]
rs73120267	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73120269	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73120297	1.00[EUR][1000 genomes]
rs851140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs851144	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851145	1.00[EUR][1000 genomes]
rs851146	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851147	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs851148	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs851150	1.00[EUR][1000 genomes]
rs851151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851152	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs851153	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs851154	1.00[EUR][1000 genomes]
rs851155	1.00[EUR][1000 genomes]
rs851156	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs851158	1.00[EUR][1000 genomes]
rs851160	0.95[ASN][1000 genomes]
rs851163	0.95[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	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs988242	0.90[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	chr1:223377000-223392200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:223386200-223391800	Weak transcription	Ovary	ovary
3	chr1:223387800-223392400	Weak transcription	Brain Anterior Caudate	brain
4	chr1:223387800-223392400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:223389000-223390400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:223389400-223390600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:223389600-223390200	Enhancers	Fetal Brain Male	brain
8	chr1:223389600-223390600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:223389600-223390800	Enhancers	Fetal Muscle Leg	muscle
10	chr1:223389800-223390000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:223389800-223390200	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:223389800-223390400	Enhancers	Gastric	stomach

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