Variant report

Variant	rs422854
Chromosome Location	chr2:39185048-39185049
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	chr2:39183680..39185526-chr2:39186357..39188173,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269210	Chromatin interaction
ENSG00000214694	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10166801	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap]
rs10172714	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10177250	0.92[CHB][hapmap]
rs10183915	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs10186762	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10192250	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10194374	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap]
rs10201980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1037495	0.85[CHB][hapmap]
rs1043793	1.00[CHB][hapmap]
rs10779924	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12471731	0.92[CHB][hapmap]
rs12712630	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs13023273	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1377860	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1454221	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1454222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1454223	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1454225	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1454226	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs1470915	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs1531021	0.83[EUR][1000 genomes]
rs1869513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1869514	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1947432	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2123876	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2123879	0.85[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2123881	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs2168042	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs2168044	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2278912	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2278913	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278914	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2290445	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2373495	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap]
rs2373496	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2603145	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2888585	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs297135	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap]
rs297148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs297149	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs297150	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs297151	0.87[CEU][hapmap]
rs297152	0.87[CEU][hapmap]
rs297153	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs297158	0.87[CEU][hapmap];0.84[CHB][hapmap]
rs297159	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs297160	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs371745	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3765058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs378698	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap]
rs4142729	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4643520	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4670269	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs4670270	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4670272	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs4670901	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670902	0.84[CHB][hapmap]
rs4670903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6544183	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544184	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6544185	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6544187	0.86[AMR][1000 genomes]
rs6544197	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs6704656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6713281	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6716101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs672208	0.84[ASN][1000 genomes]
rs6725356	0.82[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6739568	0.84[CHB][hapmap]
rs6752850	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6755527	0.86[AMR][1000 genomes]
rs6756184	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap]
rs7571052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7573310	0.93[AMR][1000 genomes]
rs7577088	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7582918	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7594644	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs963730	0.91[CHB][hapmap]
rs963731	0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs9679498	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs997344	0.84[CHB][hapmap];0.80[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	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs422854	SOS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39110200-39186800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:39150000-39186600	Weak transcription	Brain Anterior Caudate	brain
3	chr2:39160400-39186600	Weak transcription	Pancreas	Pancrea
4	chr2:39175000-39186600	Weak transcription	Ovary	ovary
5	chr2:39175000-39187000	Weak transcription	Brain Angular Gyrus	brain
6	chr2:39175200-39186800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:39176600-39186600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:39184200-39185600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:39184600-39186600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:39184800-39185400	Enhancers	Psoas Muscle	Psoas
11	chr2:39184800-39185400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:39184800-39185600	Enhancers	Skeletal Muscle Male	skeletal muscle

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