Variant report

Variant	rs4709396
Chromosome Location	chr6:160497890-160497891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:160496060..160498453-chr6:160518764..160521652,3	K562	blood:
2	chr6:160497364..160500238-chr6:160505047..160507278,2	K562	blood:

Variant related genes	Relation type
ENSG00000197081	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1803989	0.81[EUR][1000 genomes]
rs1805075	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867350	1.00[ASW][hapmap];0.93[MEX][hapmap]
rs1871388	1.00[ASW][hapmap]
rs2274849	0.90[ASN][1000 genomes]
rs2282138	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2282139	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2297362	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2297366	0.84[AMR][1000 genomes]
rs28633601	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777409	0.82[CEU][hapmap];0.90[CHB][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777412	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3798168	1.00[ASW][hapmap];0.93[MEX][hapmap]
rs3798177	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4708856	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56262344	0.98[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56296641	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57905622	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58444339	0.84[EUR][1000 genomes]
rs60210682	0.81[EUR][1000 genomes]
rs73023681	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7746102	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8191816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8191818	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8191821	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8191829	0.90[ASN][1000 genomes]
rs8191832	0.90[ASN][1000 genomes]
rs8191847	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8191898	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9457827	0.89[CEU][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv1004150	chr6:160493668-160499709	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4709396	GALNT9	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160444200-160521600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:160453000-160534600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:160455800-160532000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:160459200-160501200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:160459600-160519200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:160460600-160500800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:160460800-160520200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:160460800-160520200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:160461000-160500600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:160461200-160500800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:160464400-160519800	Strong transcription	Lung	lung
12	chr6:160464600-160531800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:160465600-160530800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:160466000-160521000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:160474200-160501200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr6:160474200-160519600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:160474200-160519800	Strong transcription	Fetal Stomach	stomach
18	chr6:160474400-160520600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr6:160474800-160509200	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr6:160474800-160509400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:160477200-160531200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:160477200-160531400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:160479400-160499200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:160480200-160510600	Strong transcription	Fetal Intestine Large	intestine
25	chr6:160480600-160502800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr6:160485000-160512600	Weak transcription	Right Atrium	heart
27	chr6:160485600-160501800	Strong transcription	Placenta	Placenta
28	chr6:160485800-160522800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:160487400-160498000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:160487600-160498000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:160487600-160498200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:160487600-160498400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr6:160487600-160503000	Strong transcription	K562	blood
34	chr6:160487600-160503800	Strong transcription	Osteobl	bone
35	chr6:160487600-160509400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:160487600-160520000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:160487600-160530800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:160487800-160498400	Strong transcription	Brain Angular Gyrus	brain
39	chr6:160487800-160500200	Strong transcription	HepG2	liver
40	chr6:160487800-160501000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:160487800-160501000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:160487800-160502000	Strong transcription	NHEK	skin
43	chr6:160487800-160502800	Strong transcription	Left Ventricle	heart
44	chr6:160487800-160509000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr6:160487800-160509200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:160487800-160509400	Strong transcription	Brain Hippocampus Middle	brain
47	chr6:160487800-160515600	Strong transcription	Right Ventricle	heart
48	chr6:160487800-160519200	Strong transcription	Esophagus	oesophagus
49	chr6:160487800-160519400	Strong transcription	Gastric	stomach
50	chr6:160487800-160519800	Strong transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links