Variant report

Variant	rs4233654
Chromosome Location	chr2:152596011-152596012
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152582502..152584750-chr2:152594668..152596852,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10165921	0.85[JPT][hapmap]
rs10170273	0.85[GIH][hapmap]
rs10171724	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10172692	0.82[ASN][1000 genomes]
rs10178880	0.82[GIH][hapmap]
rs10180065	0.94[ASN][1000 genomes]
rs10184063	0.86[ASN][1000 genomes]
rs10185966	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10198530	0.82[ASN][1000 genomes]
rs10198531	0.84[ASN][1000 genomes]
rs10754989	0.84[ASN][1000 genomes]
rs11682909	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs11894672	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[ASN][1000 genomes]
rs11896217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464543	0.81[CHD][hapmap]
rs12470190	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12472627	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs12618063	0.87[GIH][hapmap]
rs12620077	0.82[GIH][hapmap]
rs12693116	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1523181	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs16830418	1.00[CEU][hapmap]
rs1916301	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1916302	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2030588	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2293221	0.86[ASN][1000 genomes]
rs3768658	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs3922996	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3922997	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4266011	0.88[ASN][1000 genomes]
rs4300824	0.89[GIH][hapmap];0.85[JPT][hapmap]
rs4306714	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4316939	0.85[JPT][hapmap]
rs4393745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4414677	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[ASN][1000 genomes]
rs4450595	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4453694	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4510224	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4536649	0.82[GIH][hapmap]
rs4552188	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4605370	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4664066	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4664494	0.82[GIH][hapmap]
rs4664498	0.92[GIH][hapmap];0.85[JPT][hapmap]
rs4664499	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433680	1.00[CEU][hapmap]
rs6711382	0.88[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs6712443	0.87[GIH][hapmap]
rs6712533	0.87[GIH][hapmap]
rs6715027	0.93[ASN][1000 genomes]
rs6715607	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6716286	0.81[CHD][hapmap]
rs6718439	0.86[ASN][1000 genomes]
rs6740508	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6741567	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6743968	1.00[CEU][hapmap]
rs6749823	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6755393	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs6759419	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7424335	0.92[GIH][hapmap];0.95[JPT][hapmap]
rs7426114	0.82[GIH][hapmap]
rs7557801	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7564024	0.83[GIH][hapmap]
rs7564630	0.94[ASN][1000 genomes]
rs7580820	0.83[ASN][1000 genomes]
rs7581532	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7583060	0.94[ASN][1000 genomes]
rs7583148	0.94[ASN][1000 genomes]
rs7592798	0.87[ASN][1000 genomes]
rs9287998	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288006	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152584800-152610400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:152595400-152597200	ZNF genes & repeats	Aorta	Aorta
3	chr2:152595600-152596800	ZNF genes & repeats	Left Ventricle	heart
4	chr2:152595800-152620200	Weak transcription	Primary B cells from cord blood	blood
5	chr2:152596000-152596200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:152596000-152598800	Weak transcription	Psoas Muscle	Psoas
7	chr2:152596000-152600800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:152596000-152603000	Weak transcription	Placenta	Placenta

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