Variant report

Variant	rs4709399
Chromosome Location	chr6:160539046-160539047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr6:160539018-160539400	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:160534504..160540683-chr6:160541496..160546529,8	K562	blood:
2	chr6:160528947..160531777-chr6:160539028..160541745,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC22A2-1	chr6:160538218-160539659	XLOC_005902

No data

Variant related genes	Relation type
SLC22A1	TF binding region
ENSG00000270949	Chromatin interaction
ENSG00000175003	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1479355	0.83[ASN][1000 genomes]
rs1867351	0.83[CEU][hapmap]
rs2297369	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297370	0.84[CEU][hapmap]
rs2297371	0.83[CEU][hapmap]
rs2297372	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3798173	0.83[CEU][hapmap]
rs3822841	0.83[CEU][hapmap]
rs4646272	0.81[ASN][1000 genomes]
rs4709400	0.84[CEU][hapmap];0.87[ASN][1000 genomes]
rs6900842	0.82[ASN][1000 genomes]
rs6935207	0.84[CEU][hapmap];0.87[ASN][1000 genomes]
rs755884	1.00[CEU][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753051	0.81[ASN][1000 genomes]
rs7769472	0.84[CEU][hapmap]
rs9346808	0.83[ASN][1000 genomes]
rs9365131	0.83[ASN][1000 genomes]
rs9457841	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][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	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160512000-160539200	Weak transcription	Stomach Mucosa	stomach
2	chr6:160523200-160540200	Weak transcription	Fetal Heart	heart
3	chr6:160526200-160548600	Weak transcription	K562	blood
4	chr6:160526800-160540600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:160526800-160545000	Weak transcription	HMEC	breast
6	chr6:160527000-160545000	Weak transcription	NHDF-Ad	bronchial
7	chr6:160527200-160541200	Weak transcription	Osteobl	bone
8	chr6:160527400-160549200	Weak transcription	Colonic Mucosa	Colon
9	chr6:160527400-160550000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:160527600-160541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:160529000-160539600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:160529400-160548000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:160529400-160559200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:160530400-160548600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:160530600-160543000	Weak transcription	Fetal Lung	lung
16	chr6:160530800-160542800	Weak transcription	Right Atrium	heart
17	chr6:160530800-160553400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:160531400-160545400	Weak transcription	NHLF	lung
19	chr6:160532200-160542400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:160533400-160552800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:160534000-160539800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:160534400-160541200	Weak transcription	Aorta	Aorta
23	chr6:160534400-160544200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:160534600-160540200	Weak transcription	HepG2	liver
25	chr6:160535600-160539200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:160536400-160539400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:160536400-160539800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:160536600-160539600	ZNF genes & repeats	Dnd41	blood
29	chr6:160537400-160539400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:160537600-160539600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:160537600-160539800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
32	chr6:160537600-160540200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:160537600-160540200	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr6:160537800-160539400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:160538000-160539200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
36	chr6:160538000-160539200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:160538000-160539400	Strong transcription	Gastric	stomach
38	chr6:160538000-160539400	ZNF genes & repeats	Thymus	Thymus
39	chr6:160538000-160539400	ZNF genes & repeats	Spleen	Spleen
40	chr6:160538000-160539600	Strong transcription	Right Ventricle	heart
41	chr6:160538000-160539800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:160538000-160539800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:160538000-160540200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:160538000-160540200	ZNF genes & repeats	Fetal Stomach	stomach
45	chr6:160538200-160539200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
46	chr6:160538200-160539200	Strong transcription	Brain Substantia Nigra	brain
47	chr6:160538200-160539400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
48	chr6:160538200-160539400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr6:160538200-160539400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
50	chr6:160538200-160539400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin

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