Variant report

Variant	rs12242239
Chromosome Location	chr10:26973071-26973072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:26972585..26978071-chr10:26984536..26988033,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148459	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10128125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10128192	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];1.00[ASN][1000 genomes]
rs10829048	1.00[ASN][1000 genomes]
rs11015219	0.82[YRI][hapmap]
rs11015220	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015221	0.96[AFR][1000 genomes]
rs11015226	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11015234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11816510	0.83[ASN][1000 genomes]
rs11818450	0.83[ASN][1000 genomes]
rs12242246	0.96[AFR][1000 genomes]
rs12242414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244725	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12245051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12246285	1.00[ASN][1000 genomes]
rs12247299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12247597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12250220	0.82[YRI][hapmap]
rs12252298	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12252358	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12252368	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12255583	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12255942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12260035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12260298	1.00[ASN][1000 genomes]
rs12260466	0.96[ASN][1000 genomes]
rs12262082	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262401	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];1.00[ASN][1000 genomes]
rs12263262	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264509	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264994	0.96[AFR][1000 genomes]
rs12265505	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12265633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12265746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266764	0.96[AFR][1000 genomes]
rs12267744	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268014	0.96[AFR][1000 genomes]
rs12268883	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12269520	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17754039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17754051	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];0.96[ASN][1000 genomes]
rs1980754	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005120	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477276	0.81[ASN][1000 genomes]
rs2489564	0.81[ASN][1000 genomes]
rs34314417	0.96[ASN][1000 genomes]
rs34901510	1.00[ASN][1000 genomes]
rs35534478	1.00[ASN][1000 genomes]
rs35687107	1.00[ASN][1000 genomes]
rs35827769	1.00[ASN][1000 genomes]
rs4309054	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072558	0.82[YRI][hapmap]
rs7082973	1.00[AFR][1000 genomes]
rs7097696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72481186	1.00[AMR][1000 genomes]
rs72485013	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72485015	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72485017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72485018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72485022	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72485023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72485026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7896604	1.00[AFR][1000 genomes]
rs7899631	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7899804	0.96[AFR][1000 genomes]
rs7900674	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7906473	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920279	1.00[EUR][1000 genomes];0.96[ASN][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	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv3333006	chr10:26908323-26985227	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	23 gene(s)	inside rSNPs	diseases
4	esv1798973	chr10:26968171-27001814	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv550233	chr10:26968171-27011323	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26967000-26973800	Weak transcription	K562	blood
2	chr10:26969600-26974800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr10:26970600-26973800	Enhancers	Primary T cells from cord blood	blood
4	chr10:26970600-26974200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr10:26970600-26974400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr10:26970800-26973800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr10:26971000-26974400	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr10:26971000-26974400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr10:26971000-26974400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr10:26971600-26973400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:26971800-26973800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr10:26972000-26973200	Enhancers	Thymus	Thymus
13	chr10:26972000-26973800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:26972200-26973800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr10:26972600-26973200	Enhancers	Fetal Thymus	thymus
16	chr10:26972600-26973600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr10:26973000-26973400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:26973000-26978000	Weak transcription	Dnd41	blood

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