Variant report

Variant	rs11759284
Chromosome Location	chr6:24494517-24494518
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr6:24493774-24494586	K562	blood:	n/a	chr6:24493967-24493976 chr6:24493966-24493976 chr6:24493965-24493980
2	CTCF	chr6:24494347-24496072	SK-N-SH	brain:	n/a	n/a
3	REST	chr6:24494454-24495983	H1-neurons	neurons:	n/a	chr6:24495026-24495039
4	GATA1	chr6:24493258-24495592	PBDE	blood:	n/a	n/a
5	MAX	chr6:24494452-24496224	HepG2	liver:	n/a	chr6:24495932-24495942
6	CREB1	chr6:24494495-24496123	HepG2	liver:	n/a	n/a
7	UBTF	chr6:24494398-24496033	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24493014..24496474-chr6:24718971..24722650,4	K562	blood:
2	chr6:24493803..24496211-chr6:24773975..24776646,3	K562	blood:
3	chr6:24492199..24495699-chr6:24718792..24721987,5	K562	blood:
4	chr6:24489101..24491684-chr6:24493403..24495493,2	MCF-7	breast:
5	chr6:24487824..24490266-chr6:24492770..24497111,3	MCF-7	breast:
6	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
7	chr6:24488265..24492557-chr6:24493494..24498787,7	K562	blood:
8	chr6:24494081..24496615-chr6:24665704..24668263,2	K562	blood:
9	chr6:24491848..24494534-chr6:24497211..24499675,3	MCF-7	breast:
10	chr6:24487096..24491354-chr6:24491448..24495730,8	K562	blood:

Variant related genes	Relation type
GPLD1	TF binding region
ALDH5A1	TF binding region
ENSG00000111802	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000124532	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000112312	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10946703	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1111013	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1111014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11751325	0.85[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap]
rs11758106	0.82[EUR][1000 genomes]
rs12208521	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13218564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1772253	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs1810473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793422	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs34052391	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34517349	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35864956	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4646828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4712825	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62400473	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62400494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9461028	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv519552	chr6:24451256-24524704	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv883480	chr6:24481299-24507519	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3351586	chr6:24494123-24497171	Bivalent/Poised TSS Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11759284	ALDH5A1	cis	Muscle Skeletal	GTEx
rs11759284	HIST1H2AH	cis	parietal	SCAN
rs11759284	HIST1H2BM	cis	cerebellum	SCAN
rs11759284	ALDH5A1	cis	cerebellum	SCAN
rs11759284	ALDH5A1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24470600-24494600	Weak transcription	Left Ventricle	heart
2	chr6:24473000-24494600	Weak transcription	Ovary	ovary
3	chr6:24489800-24494600	Weak transcription	Right Atrium	heart
4	chr6:24490400-24494600	Weak transcription	Fetal Intestine Small	intestine
5	chr6:24492000-24494600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:24493200-24495000	Flanking Active TSS	K562	blood
7	chr6:24493800-24494800	Flanking Active TSS	Dnd41	blood
8	chr6:24494000-24495000	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr6:24494000-24495000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:24494000-24496000	Active TSS	Brain Angular Gyrus	brain
11	chr6:24494000-24496000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr6:24494200-24494600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:24494200-24494600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:24494200-24494600	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:24494200-24494600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:24494200-24494600	Enhancers	Fetal Brain Male	brain
17	chr6:24494200-24494600	Enhancers	A549	lung
18	chr6:24494200-24494800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr6:24494200-24494800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr6:24494200-24494800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr6:24494200-24494800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr6:24494200-24494800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr6:24494200-24494800	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr6:24494200-24494800	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr6:24494200-24494800	Flanking Active TSS	GM12878-XiMat	blood
26	chr6:24494200-24495000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr6:24494200-24495000	Flanking Active TSS	HepG2	liver
28	chr6:24494200-24495200	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr6:24494400-24494600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr6:24494400-24494600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:24494400-24494600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
32	chr6:24494400-24494600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
33	chr6:24494400-24494600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:24494400-24494600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:24494400-24494600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr6:24494400-24494600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:24494400-24494600	Active TSS	Colonic Mucosa	Colon
38	chr6:24494400-24494600	Active TSS	Duodenum Mucosa	Duodenum
39	chr6:24494400-24494600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr6:24494400-24494600	Enhancers	Fetal Intestine Large	intestine
41	chr6:24494400-24494600	Enhancers	Fetal Muscle Leg	muscle
42	chr6:24494400-24494600	Enhancers	Placenta	Placenta
43	chr6:24494400-24494600	Enhancers	Fetal Stomach	stomach
44	chr6:24494400-24494600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr6:24494400-24494600	Enhancers	Right Ventricle	heart
46	chr6:24494400-24494600	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr6:24494400-24494600	Enhancers	HSMM	muscle
48	chr6:24494400-24494600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
49	chr6:24494400-24494800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:24494400-24494800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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