Variant report

Variant	rs1800542
Chromosome Location	chr6:12292528-12292529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:12292182..12294128-chr6:12314408..12315965,2	MCF-7	breast:
2	chr6:12291605..12293839-chr6:12604176..12606069,2	MCF-7	breast:
3	chr6:12143600..12146335-chr6:12290629..12293218,2	MCF-7	breast:
4	chr6:12291231..12293200-chr6:12307475..12310312,2	K562	blood:
5	chr6:12292266..12293275-chr6:12504332..12505239,5	MCF-7	breast:
6	chr6:12292398..12292945-chr6:12602390..12603327,2	MCF-7	breast:
7	chr6:12292341..12293465-chr6:12603549..12604445,7	MCF-7	breast:
8	chr6:12291147..12293280-chr6:12600052..12602342,2	MCF-7	breast:
9	chr6:12290618..12292795-chr6:12486074..12487938,2	MCF-7	breast:
10	chr6:12292396..12293182-chr6:12605557..12606416,4	MCF-7	breast:
11	chr6:12292316..12293539-chr6:12603121..12604181,5	MCF-7	breast:
12	chr6:12289158..12291456-chr6:12291763..12294745,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000078401	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10478723	1.00[GIH][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800785	1.00[ASN][1000 genomes]
rs6458196	1.00[ASN][1000 genomes]
rs7750360	1.00[ASN][1000 genomes]
rs9296343	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462653	1.00[ASN][1000 genomes]
rs9462666	1.00[ASN][1000 genomes]
rs9471434	1.00[ASN][1000 genomes]
rs9471476	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830586	chr6:12130076-12295334	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12289000-12292800	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr6:12289400-12294200	Active TSS	Right Atrium	heart
3	chr6:12289600-12292800	Active TSS	Placenta Amnion	Placenta Amnion
4	chr6:12289600-12293000	Active TSS	HSMM	muscle
5	chr6:12289800-12292600	Active TSS	Right Ventricle	heart
6	chr6:12289800-12292800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr6:12289800-12292800	Bivalent/Poised TSS	Fetal Kidney	kidney
8	chr6:12289800-12293000	Active TSS	Pancreas	Pancrea
9	chr6:12289800-12293200	Active TSS	Aorta	Aorta
10	chr6:12289800-12293200	Active TSS	Colonic Mucosa	Colon
11	chr6:12289800-12293200	Active TSS	Psoas Muscle	Psoas
12	chr6:12290000-12292600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:12290000-12292800	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr6:12290000-12293800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:12290200-12293200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
16	chr6:12290800-12292600	Flanking Active TSS	Hela-S3	cervix
17	chr6:12290800-12292600	Flanking Active TSS	Osteobl	bone
18	chr6:12290800-12297200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
19	chr6:12291200-12292600	Active TSS	Rectal Smooth Muscle	rectum
20	chr6:12291200-12293200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:12291200-12293200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
22	chr6:12291400-12294400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:12291600-12292600	Flanking Active TSS	HSMMtube	muscle
24	chr6:12291600-12292800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:12291600-12292800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
26	chr6:12291600-12292800	Flanking Active TSS	HMEC	breast
27	chr6:12291600-12292800	Flanking Active TSS	NHEK	skin
28	chr6:12291600-12293000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
29	chr6:12291600-12293000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:12291600-12293200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:12291600-12293200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:12291600-12293200	Flanking Active TSS	GM12878-XiMat	blood
33	chr6:12291600-12293400	Active TSS	Lung	lung
34	chr6:12291600-12293600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr6:12291600-12293600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:12291600-12296600	Transcr. at gene 5' and 3'	A549	lung
37	chr6:12291800-12292600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
38	chr6:12291800-12292600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
39	chr6:12291800-12292600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:12291800-12292600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:12291800-12292600	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr6:12291800-12292600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
43	chr6:12291800-12292600	Enhancers	Stomach Mucosa	stomach
44	chr6:12291800-12292600	Flanking Active TSS	NH-A	brain
45	chr6:12291800-12292800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:12291800-12292800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
47	chr6:12291800-12293000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
48	chr6:12291800-12293200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:12291800-12293200	Flanking Active TSS	NHDF-Ad	bronchial
50	chr6:12291800-12293400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links