Variant report

Variant	rs2760118
Chromosome Location	chr6:24503590-24503591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1126617	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs12190732	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12190926	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12197859	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13193549	0.80[EUR][1000 genomes]
rs1883415	0.82[ASW][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs2076316	0.91[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs2076317	0.91[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs2245668	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2245674	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2744568	0.80[ASN][1000 genomes]
rs2744577	0.85[ASN][1000 genomes]
rs2744578	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2744579	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2744584	0.80[EUR][1000 genomes]
rs2744587	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2760114	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760115	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760116	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760117	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	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2760129	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2760131	0.81[CHB][hapmap]
rs2760140	0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2817213	0.85[ASN][1000 genomes]
rs2817216	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2817219	0.86[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817223	0.81[EUR][1000 genomes]
rs67103741	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7775073	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7775307	0.87[EUR][1000 genomes];0.86[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
rs2760118	TRIM38	cis	cerebellum	SCAN
rs2760118	ALDH5A1	Cis_1M	lymphoblastoid	RTeQTL
rs2760118	ALDH5A1	cis	cerebellum	SCAN
rs2760118	ALDH5A1	cis	lymphoblastoid	seeQTL
rs2760118	TDP2	cis	parietal	SCAN
rs2760118	ALDH5A1	cis	Thyroid	GTEx
rs2760118	ALDH5A1	cis	parietal	SCAN
rs2760118	ALDH5A1	cis	lung	GTEx

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	chr6:24496200-24503600	Weak transcription	Aorta	Aorta
7	chr6:24496200-24503600	Weak transcription	Ovary	ovary
8	chr6:24496200-24503600	Weak transcription	Pancreas	Pancrea
9	chr6:24496200-24503800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:24496200-24503800	Weak transcription	Fetal Brain Female	brain
11	chr6:24496200-24504000	Weak transcription	Fetal Lung	lung
12	chr6:24496200-24505000	Weak transcription	Right Ventricle	heart
13	chr6:24496200-24506200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:24496200-24526400	Weak transcription	Right Atrium	heart
15	chr6:24496200-24527800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:24496200-24534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:24496200-24535000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:24496200-24536200	Weak transcription	Psoas Muscle	Psoas
19	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
20	chr6:24496400-24503600	Weak transcription	Fetal Kidney	kidney
21	chr6:24496400-24503800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr6:24496400-24517200	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:24496400-24532200	Weak transcription	Brain Germinal Matrix	brain
24	chr6:24496600-24503600	Weak transcription	Brain Anterior Caudate	brain
25	chr6:24496600-24503600	Weak transcription	Left Ventricle	heart
26	chr6:24496600-24504000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:24496600-24505000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:24496600-24507000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:24496600-24507400	Weak transcription	Fetal Brain Male	brain
30	chr6:24496600-24512400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:24496800-24503600	Weak transcription	Brain Angular Gyrus	brain
32	chr6:24496800-24503600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:24496800-24507600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:24496800-24508800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:24496800-24517600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:24496800-24522800	Weak transcription	Lung	lung
37	chr6:24496800-24532400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:24497000-24507200	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:24497000-24528200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr6:24497400-24522400	Weak transcription	K562	blood
41	chr6:24497800-24503800	Weak transcription	Primary B cells from cord blood	blood
42	chr6:24498200-24507200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:24498400-24517400	Weak transcription	GM12878-XiMat	blood
44	chr6:24498800-24503600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr6:24498800-24503600	Weak transcription	Fetal Stomach	stomach
46	chr6:24498800-24512200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:24498800-24517600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:24501600-24507200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:24501800-24503600	Weak transcription	Thymus	Thymus
50	chr6:24502200-24507000	Strong transcription	Dnd41	blood

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