Variant report

Variant	rs4678409
Chromosome Location	chr3:138057719-138057720
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138048191..138050080-chr3:138056957..138059318,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181322	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1002766	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11710280	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11713141	0.88[EUR][1000 genomes]
rs1199330	0.86[JPT][hapmap]
rs1199331	0.83[EUR][1000 genomes]
rs1199332	0.80[CHD][hapmap]
rs1199338	0.83[CHD][hapmap]
rs12107581	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12490350	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13324341	0.90[CHD][hapmap]
rs1564407	0.84[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1564408	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1679147	0.87[EUR][1000 genomes]
rs1720819	0.80[CHD][hapmap]
rs1720828	0.80[CHD][hapmap]
rs2054468	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2061936	0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs2169973	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293252	0.81[EUR][1000 genomes]
rs253665	0.81[CHD][hapmap]
rs35219044	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755751	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3773752	0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773758	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773759	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816730	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678260	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678261	0.95[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678407	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4678408	0.92[CEU][hapmap];0.84[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4678410	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4678411	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4678412	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678415	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678417	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439804	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439805	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439806	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6439807	0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67559768	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6766859	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6769236	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6769261	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6782181	0.88[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs6782449	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6784989	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6789235	0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs6790398	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6802211	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6807945	0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs730158	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs731632	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs751357	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7615658	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7626388	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7626424	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7637666	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7639809	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7639850	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7642400	0.87[EUR][1000 genomes]
rs9289559	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs940233	0.81[CEU][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9825697	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9834911	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9845672	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9846198	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9846223	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9854465	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9855722	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138048600-138057800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:138055800-138058000	Weak transcription	Fetal Brain Female	brain
3	chr3:138056200-138058200	Enhancers	Fetal Muscle Trunk	muscle
4	chr3:138056200-138058400	Enhancers	HSMM	muscle
5	chr3:138056400-138057800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:138056400-138058000	Enhancers	Right Atrium	heart
7	chr3:138056400-138058200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:138056600-138058000	Enhancers	Left Ventricle	heart
9	chr3:138056600-138058400	Enhancers	Fetal Muscle Leg	muscle
10	chr3:138056600-138058400	Enhancers	HSMMtube	muscle
11	chr3:138056800-138057800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:138056800-138058200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:138056800-138058600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:138057200-138057800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:138057200-138058200	Enhancers	Ovary	ovary
16	chr3:138057400-138058000	Enhancers	Psoas Muscle	Psoas
17	chr3:138057400-138058400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:138057400-138066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:138057600-138058000	Enhancers	Pancreas	Pancrea
20	chr3:138057600-138058200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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