Variant report

Variant	rs2744586
Chromosome Location	chr6:24507676-24507677
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24504725..24507769-chr6:24719049..24722072,3	MCF-7	breast:
2	chr6:24496929..24500234-chr6:24504252..24507783,4	K562	blood:
3	chr6:24500345..24502896-chr6:24503949..24507789,3	K562	blood:
4	chr6:24495638..24500234-chr6:24504925..24509115,5	K562	blood:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2251547	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2322458	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2744570	1.00[JPT][hapmap]
rs2744574	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2744584	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2760117	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs2817214	0.81[ASN][1000 genomes]
rs2817220	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817222	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817223	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817224	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817225	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2817228	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646841	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72834958	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs807514	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs807516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs807517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9358768	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9393559	0.86[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2744586	ALDH5A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 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	chr6:24496200-24526400	Weak transcription	Right Atrium	heart
7	chr6:24496200-24527800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:24496200-24534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:24496200-24535000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:24496200-24536200	Weak transcription	Psoas Muscle	Psoas
11	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
12	chr6:24496400-24517200	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:24496400-24532200	Weak transcription	Brain Germinal Matrix	brain
14	chr6:24496600-24512400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:24496800-24508800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:24496800-24517600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:24496800-24522800	Weak transcription	Lung	lung
18	chr6:24496800-24532400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:24497000-24528200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr6:24497400-24522400	Weak transcription	K562	blood
21	chr6:24498400-24517400	Weak transcription	GM12878-XiMat	blood
22	chr6:24498800-24512200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:24498800-24517600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:24502200-24508200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr6:24502200-24510200	Strong transcription	Fetal Thymus	thymus
26	chr6:24502400-24508000	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr6:24502600-24511400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:24502800-24507800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr6:24502800-24508000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:24502800-24509200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:24503600-24507800	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:24503600-24508600	Strong transcription	Thymus	Thymus
33	chr6:24504200-24508000	Weak transcription	Small Intestine	intestine
34	chr6:24504200-24513800	Weak transcription	Aorta	Aorta
35	chr6:24504200-24522600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:24504400-24534200	Weak transcription	Pancreas	Pancrea
37	chr6:24505200-24516800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:24505400-24534000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:24505600-24516000	Weak transcription	A549	lung
40	chr6:24505800-24513400	Weak transcription	Left Ventricle	heart
41	chr6:24505800-24527800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:24505800-24530800	Weak transcription	Right Ventricle	heart
43	chr6:24505800-24534000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:24505800-24534000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:24506200-24513000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:24506400-24512200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:24506400-24512200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:24506400-24513800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:24506400-24514000	Weak transcription	Ovary	ovary
50	chr6:24506400-24530000	Weak transcription	Placenta	Placenta

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