Variant report

Variant	rs2744600
Chromosome Location	chr6:24533432-24533433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24530783..24533712-chr6:24700418..24704307,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272345	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1054899	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1091031	0.90[ASN][1000 genomes]
rs1091032	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1091033	0.86[ASN][1000 genomes]
rs2744598	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2744599	0.95[ASN][1000 genomes]
rs2744602	0.92[ASN][1000 genomes]
rs2744603	0.90[ASN][1000 genomes]
rs807530	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2744600	MRS2L	cis	multi-tissue	Pritchard
rs2744600	ALDH5A1	cis	lung	GTEx
rs2744600	GPLD1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24496000-24534200	Weak transcription	Gastric	stomach
2	chr6:24496000-24538000	Weak transcription	Esophagus	oesophagus
3	chr6:24496200-24534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:24496200-24535000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:24496200-24536200	Weak transcription	Psoas Muscle	Psoas
6	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
7	chr6:24504400-24534200	Weak transcription	Pancreas	Pancrea
8	chr6:24505400-24534000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:24505800-24534000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:24505800-24534000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:24507800-24536800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:24507800-24539200	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:24509400-24545800	Weak transcription	Small Intestine	intestine
14	chr6:24516000-24534200	Weak transcription	Brain Angular Gyrus	brain
15	chr6:24523000-24534200	Weak transcription	Lung	lung
16	chr6:24523000-24537000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:24523200-24534200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:24523200-24534200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:24523200-24534200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:24523600-24536800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:24525200-24533800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:24526400-24537000	Weak transcription	Primary B cells from cord blood	blood
23	chr6:24528400-24534200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:24528400-24537800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:24528400-24540800	Strong transcription	Liver	Liver
26	chr6:24528600-24534200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:24528800-24534400	Weak transcription	Fetal Brain Male	brain
28	chr6:24530000-24540800	Strong transcription	Thymus	Thymus
29	chr6:24530200-24535600	Strong transcription	HepG2	liver
30	chr6:24530200-24536000	Strong transcription	Primary T cells from cord blood	blood
31	chr6:24530200-24538200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:24530200-24540800	Strong transcription	Fetal Thymus	thymus
33	chr6:24530400-24535600	Strong transcription	Fetal Muscle Leg	muscle
34	chr6:24530400-24538200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:24530600-24535600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:24530600-24535600	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:24530600-24535600	Strong transcription	Dnd41	blood
38	chr6:24530600-24536000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr6:24530800-24535600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:24530800-24535600	Strong transcription	Fetal Intestine Large	intestine
41	chr6:24530800-24535600	Strong transcription	Fetal Intestine Small	intestine
42	chr6:24530800-24535800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:24531000-24535600	Strong transcription	Adipose Nuclei	Adipose
44	chr6:24531000-24535600	Strong transcription	Brain Anterior Caudate	brain
45	chr6:24531200-24535800	Weak transcription	Placenta	Placenta
46	chr6:24531400-24536400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr6:24531600-24534800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:24531600-24535800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr6:24531800-24535600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:24531800-24535600	Strong transcription	Stomach Smooth Muscle	stomach

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