Variant report

Variant	rs2760117
Chromosome Location	chr6:24504189-24504190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24493719..24496682-chr6:24502881..24505114,2	K562	blood:
2	chr6:24504155..24505791-chr6:24513770..24515648,2	K562	blood:
3	chr6:24497206..24500144-chr6:24502439..24504926,2	MCF-7	breast:
4	chr6:24501950..24504641-chr6:24720366..24723050,2	MCF-7	breast:
5	chr6:24493044..24496959-chr6:24499053..24507631,9	MCF-7	breast:
6	chr6:24478986..24481425-chr6:24502139..24505080,2	K562	blood:
7	chr6:24491857..24498070-chr6:24502018..24507031,7	MCF-7	breast:
8	chr6:24500345..24502896-chr6:24503949..24507789,3	K562	blood:
9	chr6:24502718..24505589-chr6:24714099..24715780,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1126617	0.86[ASW][hapmap];0.81[CHB][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap]
rs12190926	0.83[EUR][1000 genomes]
rs12197859	0.84[EUR][1000 genomes]
rs1883415	0.81[CHB][hapmap];0.88[MEX][hapmap]
rs2076316	0.84[CEU][hapmap];0.91[CHB][hapmap];0.83[MEX][hapmap]
rs2076317	0.84[CEU][hapmap];0.91[CHB][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2143083	0.86[ASW][hapmap];0.87[YRI][hapmap]
rs2245668	0.83[ASN][1000 genomes]
rs2245674	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2328824	0.86[ASW][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs2744578	0.81[EUR][1000 genomes]
rs2744579	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2744584	0.92[ASW][hapmap];0.82[CEU][hapmap];0.88[MEX][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2744586	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs2744587	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2760114	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760115	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760116	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760118	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760126	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2760129	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2760131	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2760140	0.85[ASW][hapmap];0.94[MEX][hapmap]
rs2760144	0.86[JPT][hapmap]
rs2817216	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2817219	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2817220	0.92[ASW][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes]
rs2817222	0.87[AFR][1000 genomes]
rs2817223	0.82[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2817224	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2817225	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67103741	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7775073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7775307	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2760117	ALDH5A1	cis	lymphoblastoid	seeQTL
rs2760117	ALDH5A1	cis	Thyroid	GTEx
rs2760117	ALDH5A1	cis	parietal	SCAN
rs2760117	ALDH5A1	cis	Muscle Skeletal	GTEx
rs2760117	ALDH5A1	cis	cerebellum	SCAN
rs2760117	ALDH5A1	cis	lung	GTEx
rs2760117	ALDH5A1	cis	multi-tissue	Pritchard
rs2760117	TDP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24495800-24517800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:24496000-24513000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:24496000-24517800	Weak transcription	Spleen	Spleen
4	chr6:24496000-24534200	Weak transcription	Gastric	stomach
5	chr6:24496000-24538000	Weak transcription	Esophagus	oesophagus
6	chr6:24496200-24505000	Weak transcription	Right Ventricle	heart
7	chr6:24496200-24506200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:24496200-24526400	Weak transcription	Right Atrium	heart
9	chr6:24496200-24527800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:24496200-24534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:24496200-24535000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:24496200-24536200	Weak transcription	Psoas Muscle	Psoas
13	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
14	chr6:24496400-24517200	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:24496400-24532200	Weak transcription	Brain Germinal Matrix	brain
16	chr6:24496600-24505000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:24496600-24507000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:24496600-24507400	Weak transcription	Fetal Brain Male	brain
19	chr6:24496600-24512400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:24496800-24507600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:24496800-24508800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr6:24496800-24517600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:24496800-24522800	Weak transcription	Lung	lung
24	chr6:24496800-24532400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:24497000-24507200	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:24497000-24528200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:24497400-24522400	Weak transcription	K562	blood
28	chr6:24498200-24507200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:24498400-24517400	Weak transcription	GM12878-XiMat	blood
30	chr6:24498800-24512200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:24498800-24517600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:24501600-24507200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:24502200-24507000	Strong transcription	Dnd41	blood
34	chr6:24502200-24507600	Strong transcription	Primary T cells from cord blood	blood
35	chr6:24502200-24508200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr6:24502200-24510200	Strong transcription	Fetal Thymus	thymus
37	chr6:24502400-24506400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:24502400-24508000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr6:24502600-24507000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:24502600-24511400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:24502800-24504400	Strong transcription	Liver	Liver
42	chr6:24502800-24504800	Weak transcription	A549	lung
43	chr6:24502800-24505200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr6:24502800-24506400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:24502800-24507800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr6:24502800-24508000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:24502800-24509200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:24503000-24506000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:24503200-24506400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr6:24503200-24507600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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