Variant report

Variant	rs12206069
Chromosome Location	chr6:144014595-144014596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143996710..144001910-chr6:144005817..144014875,10	MCF-7	breast:
2	chr6:144011351..144015622-chr6:144016784..144019989,3	K562	blood:
3	chr6:144009959..144011502-chr6:144013449..144016270,2	K562	blood:

Variant related genes	Relation type
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10872562	0.87[ASN][1000 genomes]
rs1108314	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11155317	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12198291	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12207002	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12208927	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12528456	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3924969	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6901659	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6907410	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6913134	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6915784	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7740709	0.81[ASN][1000 genomes]
rs7741424	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7766510	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7776119	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8180640	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9373396	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9376776	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9376779	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9386042	0.82[ASN][1000 genomes]
rs9390126	0.86[ASN][1000 genomes]
rs9399458	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403521	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9403523	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv886737	chr6:144010570-144033992	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144003600-144015000	Weak transcription	Esophagus	oesophagus
2	chr6:144003600-144015000	Weak transcription	Gastric	stomach
3	chr6:144005000-144020400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:144005600-144016000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:144005800-144015200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:144006000-144017800	Weak transcription	Fetal Heart	heart
7	chr6:144008600-144015000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:144008800-144015000	Weak transcription	NHEK	skin
9	chr6:144009000-144015200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:144009200-144015000	Weak transcription	HMEC	breast
11	chr6:144009200-144016200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:144009400-144015600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr6:144009400-144016600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:144009600-144015000	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:144010200-144015200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:144010200-144019600	Weak transcription	Spleen	Spleen
17	chr6:144010400-144015000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:144010400-144017800	Weak transcription	Ovary	ovary
19	chr6:144010400-144020000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:144011200-144016200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:144011400-144016000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:144011600-144015000	Weak transcription	Lung	lung
23	chr6:144011600-144015600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:144011600-144053200	Weak transcription	Hela-S3	cervix
25	chr6:144011800-144015000	Weak transcription	Left Ventricle	heart
26	chr6:144011800-144015400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:144011800-144015600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:144011800-144015600	Weak transcription	NH-A	brain
29	chr6:144011800-144016000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:144011800-144017600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:144011800-144019600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:144011800-144019800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:144012000-144015600	Weak transcription	HSMM	muscle
34	chr6:144012200-144014800	Weak transcription	HUVEC	blood vessel
35	chr6:144012200-144018600	Enhancers	Stomach Mucosa	stomach
36	chr6:144012200-144026800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:144012400-144018000	Enhancers	Fetal Stomach	stomach
38	chr6:144012800-144016600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:144013200-144014800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:144013200-144015000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr6:144013200-144017600	Weak transcription	Osteobl	bone
42	chr6:144013400-144014600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:144013400-144014800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:144013400-144014800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:144013400-144014800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:144013400-144014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:144013400-144015400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:144013400-144016200	Weak transcription	Adipose Nuclei	Adipose
49	chr6:144013400-144016600	Weak transcription	Brain Hippocampus Middle	brain
50	chr6:144013400-144017000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links