Variant report

Variant	rs2744597
Chromosome Location	chr6:24533074-24533075
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: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12055519	0.83[AFR][1000 genomes]
rs1569579	0.82[MEX][hapmap]
rs2247845	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2744572	0.85[MEX][hapmap]
rs2744593	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2744594	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2760138	0.81[MEX][hapmap]
rs2760186	0.81[EUR][1000 genomes]
rs2817232	0.84[EUR][1000 genomes]
rs2817233	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3761789	0.83[AFR][1000 genomes]
rs807510	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs807513	0.80[AMR][1000 genomes]
rs807518	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs807519	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs807527	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs807529	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs807531	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs807532	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs807538	0.87[AMR][1000 genomes]
rs807540	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs807542	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs807543	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9393563	0.84[AMR][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2744597	FAM65B	cis	cerebellum	SCAN
rs2744597	MRS2	cis	parietal	SCAN
rs2744597	HIST1H4E	cis	parietal	SCAN
rs2744597	HIST1H4C	cis	parietal	SCAN
rs2744597	ZNF165	cis	cerebellum	SCAN

Chromatin state (count:76 , 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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