Variant report

Variant	rs2667120
Chromosome Location	chr4:142943485-142943486
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	chr4:142942418..142944888-chr4:142957295..142959081,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10018891	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10519621	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs173060	0.90[EUR][1000 genomes]
rs1845971	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1912713	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs1912714	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1912715	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1988510	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1988511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645809	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2645825	1.00[EUR][1000 genomes]
rs2645827	1.00[CEU][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2645828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667082	1.00[EUR][1000 genomes]
rs2667087	1.00[CEU][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2667088	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2667089	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2667090	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2667091	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs336337	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs336338	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs336339	1.00[CEU][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs336340	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs336341	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs336343	1.00[EUR][1000 genomes]
rs336344	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs336345	0.82[CEU][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs336347	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs336348	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs336351	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336352	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336354	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336355	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336356	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336357	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336358	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336359	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336360	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs336362	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs336363	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337232	0.90[EUR][1000 genomes]
rs6848572	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830096	chr4:142867099-143023761	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv428775	chr4:142943213-143050195	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr4:142940600-142948400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:142941800-142957800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:142942000-142953200	Weak transcription	Right Ventricle	heart
4	chr4:142942200-142949000	Weak transcription	Primary T cells from cord blood	blood
5	chr4:142942200-142949000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:142942400-142949200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:142942800-142945000	Enhancers	Stomach Mucosa	stomach
8	chr4:142943000-142944000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr4:142943000-142944200	Enhancers	Fetal Intestine Small	intestine
10	chr4:142943200-142944000	Enhancers	Fetal Intestine Large	intestine
11	chr4:142943200-142945600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:142943400-142949000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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