Variant report

Variant	rs9399458
Chromosome Location	chr6:144014397-144014398
allele	C/T
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: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10872562	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1108314	0.93[ASN][1000 genomes]
rs11155317	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12198291	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12206069	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12207002	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12208927	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12528456	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3924969	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6901659	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6907410	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913134	0.90[ASN][1000 genomes]
rs6915784	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7740709	0.86[ASN][1000 genomes]
rs7741424	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7766510	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7772565	0.80[ASN][1000 genomes]
rs7776119	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8180640	0.93[ASN][1000 genomes]
rs9373396	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9376776	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9376779	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9386042	0.87[ASN][1000 genomes]
rs9390126	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9403521	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403523	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[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:88 , 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	chr6:144011200-144014400	Enhancers	Fetal Lung	lung
21	chr6:144011200-144016200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:144011400-144016000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:144011600-144015000	Weak transcription	Lung	lung
24	chr6:144011600-144015600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:144011600-144053200	Weak transcription	Hela-S3	cervix
26	chr6:144011800-144015000	Weak transcription	Left Ventricle	heart
27	chr6:144011800-144015400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:144011800-144015600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:144011800-144015600	Weak transcription	NH-A	brain
30	chr6:144011800-144016000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:144011800-144017600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:144011800-144019600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:144011800-144019800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:144012000-144015600	Weak transcription	HSMM	muscle
35	chr6:144012200-144014800	Weak transcription	HUVEC	blood vessel
36	chr6:144012200-144018600	Enhancers	Stomach Mucosa	stomach
37	chr6:144012200-144026800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:144012400-144018000	Enhancers	Fetal Stomach	stomach
39	chr6:144012800-144014400	Enhancers	Fetal Intestine Large	intestine
40	chr6:144012800-144016600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:144013000-144014400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr6:144013200-144014400	Enhancers	Fetal Intestine Small	intestine
43	chr6:144013200-144014400	Flanking Active TSS	HepG2	liver
44	chr6:144013200-144014800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:144013200-144015000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:144013200-144017600	Weak transcription	Osteobl	bone
47	chr6:144013400-144014600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:144013400-144014800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:144013400-144014800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:144013400-144014800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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