Variant report

Variant	rs12299499
Chromosome Location	chr12:46833979-46833980
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46832578..46835564-chr12:46837748..46840595,2	K562	blood:
2	chr12:46832724..46834258-chr12:46883859..46885941,2	MCF-7	breast:
3	chr12:46762033..46769988-chr12:46831671..46842896,19	MCF-7	breast:
4	chr12:46760616..46768014-chr12:46824033..46835241,16	K562	blood:
5	chr12:46831045..46834457-chr12:46835919..46840293,4	MCF-7	breast:
6	chr12:46831996..46834335-chr12:46842216..46844233,3	MCF-7	breast:
7	chr12:46764063..46766992-chr12:46830927..46834019,4	K562	blood:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10467215	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs10506267	0.93[CHB][hapmap]
rs11183454	0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11183467	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11183482	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183487	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183500	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs11183510	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1125908	0.83[CHB][hapmap];1.00[AMR][1000 genomes]
rs11830080	1.00[EUR][1000 genomes]
rs11834905	1.00[AMR][1000 genomes]
rs11837634	1.00[EUR][1000 genomes]
rs12314541	0.84[YRI][hapmap]
rs12317255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12320438	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321512	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12321642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321960	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs12322378	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13377959	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17096884	0.84[CHB][hapmap];1.00[AMR][1000 genomes]
rs17096896	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17096922	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];0.85[ASN][1000 genomes]
rs17096998	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs2085682	1.00[EUR][1000 genomes]
rs2125646	0.84[CHB][hapmap]
rs2307062	0.84[CHB][hapmap]
rs2307063	0.85[CHB][hapmap]
rs2408509	0.84[CHB][hapmap]
rs34280632	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35875247	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36010856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3742061	0.85[CHB][hapmap];1.00[AMR][1000 genomes]
rs3935048	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs4768118	1.00[YRI][hapmap]
rs56036156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56160202	1.00[EUR][1000 genomes]
rs56196954	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56314009	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57425661	1.00[AMR][1000 genomes]
rs58460251	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58890669	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59608605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60565802	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60878594	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61406609	1.00[AMR][1000 genomes]
rs73282591	1.00[AMR][1000 genomes]
rs73290315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74082237	1.00[EUR][1000 genomes]
rs74082254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74082263	1.00[EUR][1000 genomes]
rs74082274	1.00[EUR][1000 genomes]
rs74083758	1.00[EUR][1000 genomes]
rs7488027	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7953339	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7954314	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7965618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7967889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7977319	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7980023	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs923788	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9669404	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46821600-46848600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:46825400-46844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:46825600-46843800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:46826400-46836000	Weak transcription	NH-A	brain
5	chr12:46826400-46839200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:46826600-46836400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:46826800-46836000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:46828000-46835800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:46828000-46856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:46830600-46834800	Enhancers	HUVEC	blood vessel
11	chr12:46831200-46838200	Weak transcription	K562	blood
12	chr12:46831200-46843200	Weak transcription	Left Ventricle	heart
13	chr12:46831600-46836000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:46832600-46834600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:46832600-46834600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:46832600-46836000	Enhancers	NHEK	skin
17	chr12:46832600-46836200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:46832800-46837200	Weak transcription	Pancreas	Pancrea
19	chr12:46832800-46837400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:46833600-46834000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr12:46833600-46834000	Flanking Active TSS	Hela-S3	cervix
22	chr12:46833600-46834400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:46833600-46834400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:46833600-46834400	Enhancers	HMEC	breast
25	chr12:46833600-46834400	Enhancers	NHDF-Ad	bronchial
26	chr12:46833600-46834400	Enhancers	Osteobl	bone
27	chr12:46833600-46834600	Enhancers	NHLF	lung
28	chr12:46833600-46840800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:46833800-46834000	Enhancers	Esophagus	oesophagus
30	chr12:46833800-46834400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:46833800-46834400	Enhancers	A549	lung
32	chr12:46833800-46834400	Enhancers	HSMM	muscle

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