Variant report

Variant	rs2744294
Chromosome Location	chr6:25296606-25296607
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	chr6:25288747..25291060-chr6:25294268..25296808,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2018839	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2064206	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2690041	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2690110	0.85[JPT][hapmap];0.88[LWK][hapmap];0.81[MKK][hapmap]
rs2690117	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690118	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2690132	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690134	0.86[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2690135	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744267	0.81[TSI][hapmap]
rs2744288	0.86[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744289	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744293	0.92[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744297	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2744300	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914799	0.82[CHD][hapmap]
rs6926126	0.82[CHD][hapmap]
rs7741111	0.81[ASN][1000 genomes]
rs7752524	0.94[LWK][hapmap]
rs7764258	0.88[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	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
rs2744294	HIST1H3B	cis	cerebellum	SCAN
rs2744294	SLC17A1	cis	parietal	SCAN
rs2744294	HIST1H3G	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25286800-25300800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:25288600-25301200	Weak transcription	Brain Anterior Caudate	brain
4	chr6:25289000-25298600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:25289000-25300600	Weak transcription	Pancreas	Pancrea
6	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:25292200-25303000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:25292400-25301000	Weak transcription	Adipose Nuclei	Adipose
9	chr6:25293000-25301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:25293200-25301200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:25293800-25298000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:25294200-25311200	Weak transcription	Lung	lung
13	chr6:25294400-25297000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:25294600-25297600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:25294600-25301600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:25295000-25297800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:25295400-25297400	Enhancers	Duodenum Mucosa	Duodenum
18	chr6:25295600-25297000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:25295600-25297000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr6:25295600-25297600	Enhancers	NHLF	lung
21	chr6:25295600-25299400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:25295800-25296800	Enhancers	Fetal Intestine Large	intestine
23	chr6:25295800-25297000	Enhancers	Esophagus	oesophagus
24	chr6:25295800-25297000	Enhancers	Right Atrium	heart
25	chr6:25295800-25297000	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:25295800-25297000	Enhancers	HMEC	breast
27	chr6:25295800-25297200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:25295800-25297400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:25295800-25297800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:25295800-25297800	Enhancers	Thymus	Thymus
31	chr6:25295800-25298000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:25295800-25298000	Enhancers	Fetal Intestine Small	intestine
33	chr6:25295800-25298000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr6:25295800-25298000	Enhancers	Small Intestine	intestine
35	chr6:25295800-25298000	Enhancers	NHDF-Ad	bronchial
36	chr6:25295800-25298200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:25295800-25298200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:25295800-25298200	Enhancers	Fetal Heart	heart
39	chr6:25295800-25298200	Enhancers	HSMMtube	muscle
40	chr6:25295800-25299200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr6:25296000-25296800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:25296000-25296800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr6:25296000-25296800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:25296000-25296800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:25296000-25296800	Enhancers	Right Ventricle	heart
46	chr6:25296000-25297200	Enhancers	Primary B cells from peripheral blood	blood
47	chr6:25296000-25297200	Enhancers	Primary T cells from cord blood	blood
48	chr6:25296000-25297400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr6:25296000-25297600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr6:25296000-25297600	Enhancers	Aorta	Aorta

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