Variant report

Variant	rs6672256
Chromosome Location	chr1:209894043-209894044
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209893922..209895818-chr1:210001055..210002815,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-G0S2-3	chr1:209894009-209894546	NONHSAT009228
2	lnc-G0S2-3	chr1:209894009-209894141	NONHSAT009229

Variant related genes	Relation type
ENSG00000117597	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1000282	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1000283	1.00[ASW][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157973	0.87[EUR][1000 genomes]
rs10863783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863785	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11119327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119328	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119330	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119332	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119336	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11119340	1.00[MEX][hapmap]
rs11119341	0.93[MEX][hapmap]
rs11485195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11487866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11487867	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11806703	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11807619	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11808690	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11811440	0.87[CEU][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12030655	0.86[EUR][1000 genomes]
rs12034758	0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12059226	0.92[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12060420	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12060922	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12086634	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12090931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12094117	1.00[ASW][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];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12116437	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12120361	0.92[ASW][hapmap];0.96[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129718	0.91[EUR][1000 genomes]
rs12138452	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1337531	0.90[EUR][1000 genomes]
rs1415542	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1415544	0.91[EUR][1000 genomes]
rs1474654	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474655	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015169	0.82[MEX][hapmap]
rs17389184	0.93[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17389198	0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1999826	0.92[EUR][1000 genomes]
rs2064148	0.90[EUR][1000 genomes]
rs2205985	0.89[EUR][1000 genomes]
rs2236903	0.90[EUR][1000 genomes]
rs2272867	0.94[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2282738	0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2282739	0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs2282741	0.90[EUR][1000 genomes]
rs2884090	0.90[EUR][1000 genomes]
rs3753606	0.82[MEX][hapmap]
rs3765240	0.92[EUR][1000 genomes]
rs3766618	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3766619	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3817821	0.84[EUR][1000 genomes]
rs4314885	0.89[EUR][1000 genomes]
rs4844891	0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs61820570	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627670	0.88[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs6540549	0.82[TSI][hapmap]
rs6540550	0.87[EUR][1000 genomes]
rs6540551	0.87[EUR][1000 genomes]
rs6540552	0.85[EUR][1000 genomes]
rs6540553	0.85[EUR][1000 genomes]
rs6540554	0.82[MEX][hapmap]
rs6665715	0.88[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs667681	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6679099	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6679405	0.85[EUR][1000 genomes]
rs6702301	0.87[EUR][1000 genomes]
rs6752	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs679846	0.83[EUR][1000 genomes]
rs7521461	0.85[EUR][1000 genomes]
rs7532324	0.85[EUR][1000 genomes]
rs7539852	0.85[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7548781	0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7555978	0.87[EUR][1000 genomes]
rs909710	1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs932335	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9430012	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9430014	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9430015	0.90[EUR][1000 genomes]
rs9430016	0.85[CHD][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs9430017	0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1004343	chr1:209879304-209909385	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv525445	chr1:209885318-209912593	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209886400-209896400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:209889000-209896800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:209891600-209894400	Weak transcription	Left Ventricle	heart
4	chr1:209892400-209897000	Enhancers	Liver	Liver
5	chr1:209892800-209895600	Enhancers	Ovary	ovary
6	chr1:209893200-209895600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:209893400-209898000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:209893600-209894600	Enhancers	Fetal Heart	heart
9	chr1:209893600-209894800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:209893600-209895000	Enhancers	Osteobl	bone
11	chr1:209893600-209895200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:209893600-209899000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:209893800-209894200	Enhancers	Adipose Nuclei	Adipose
14	chr1:209893800-209895600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:209894000-209898200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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