Variant report

Variant	rs60501074
Chromosome Location	chr6:12589211-12589212
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:12589109-12589519	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000234015	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10046276	1.00[EUR][1000 genomes]
rs11750980	1.00[EUR][1000 genomes]
rs11966877	1.00[EUR][1000 genomes]
rs12332919	1.00[EUR][1000 genomes]
rs1334306	1.00[EUR][1000 genomes]
rs1334307	1.00[EUR][1000 genomes]
rs2490446	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2490448	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2490450	1.00[EUR][1000 genomes]
rs2490451	1.00[EUR][1000 genomes]
rs2504866	1.00[EUR][1000 genomes]
rs2504889	1.00[EUR][1000 genomes]
rs2504893	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2504896	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2516229	1.00[EUR][1000 genomes]
rs2516230	1.00[EUR][1000 genomes]
rs2516236	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2516237	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57317303	1.00[EUR][1000 genomes]
rs59901827	1.00[EUR][1000 genomes]
rs60493852	1.00[EUR][1000 genomes]
rs6458322	1.00[EUR][1000 genomes]
rs6900340	1.00[EUR][1000 genomes]
rs6916851	1.00[EUR][1000 genomes]
rs6928058	1.00[EUR][1000 genomes]
rs6933484	1.00[EUR][1000 genomes]
rs73356106	1.00[EUR][1000 genomes]
rs73356116	1.00[EUR][1000 genomes]
rs73356122	1.00[EUR][1000 genomes]
rs73356124	1.00[EUR][1000 genomes]
rs73722796	1.00[EUR][1000 genomes]
rs7738584	1.00[EUR][1000 genomes]
rs9462819	1.00[EUR][1000 genomes]
rs9462825	1.00[EUR][1000 genomes]
rs9462830	1.00[EUR][1000 genomes]
rs9462834	1.00[EUR][1000 genomes]
rs9471867	1.00[EUR][1000 genomes]
rs9471922	1.00[EUR][1000 genomes]
rs9471924	1.00[EUR][1000 genomes]
rs9472012	1.00[EUR][1000 genomes]
rs9472013	1.00[EUR][1000 genomes]
rs9472037	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472109	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472110	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472123	1.00[EUR][1000 genomes]
rs9472198	1.00[EUR][1000 genomes]
rs9717503	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][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	nsv470801	chr6:12559239-12666093	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv462638	chr6:12569231-12651249	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv600991	chr6:12569231-12651249	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12574000-12594600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:12580000-12592800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:12586400-12589800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:12586400-12595600	Weak transcription	Left Ventricle	heart
5	chr6:12587200-12593400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:12587200-12594000	Weak transcription	Pancreas	Pancrea
7	chr6:12587400-12592200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:12587400-12592200	Weak transcription	HMEC	breast
9	chr6:12587400-12592800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:12587400-12592800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:12587400-12592800	Weak transcription	Placenta	Placenta
12	chr6:12587400-12594200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:12587600-12592800	Weak transcription	NHEK	skin
14	chr6:12587600-12593200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:12587600-12594800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:12588200-12589400	Enhancers	A549	lung
17	chr6:12588400-12593000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr6:12588400-12593200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:12588600-12589400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:12588800-12592800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:12588800-12594000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:12588800-12594000	Weak transcription	Fetal Intestine Small	intestine
23	chr6:12589000-12589800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:12589200-12589600	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links