Variant report

Variant	rs2744288
Chromosome Location	chr6:25289063-25289064
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr6:25288943-25289133	MCF10A-Er-Src	breast:	n/a	chr6:25289039-25289047

No.	Distal block	Cell Line	Cell type
1	chr6:25281539..25283439-chr6:25288987..25290697,2	K562	blood:
2	chr6:25282721..25284707-chr6:25287856..25289519,2	MCF-7	breast:
3	chr6:25288747..25291060-chr6:25294268..25296808,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207286	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2018839	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2064206	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690041	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2690118	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2690132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2690134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690135	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744267	0.81[TSI][hapmap]
rs2744289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744293	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744294	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]
rs2744297	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744300	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914799	0.82[CHD][hapmap]
rs6926126	0.82[CHD][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
rs2744288	HIST1H3G	cis	parietal	SCAN
rs2744288	SLC17A1	cis	parietal	SCAN
rs2744288	HIST1H3B	cis	cerebellum	SCAN

Chromatin state (count:60 , 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	chr6:25281200-25290400	Weak transcription	Ovary	ovary
3	chr6:25281200-25290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:25281200-25293600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:25281200-25296000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:25281400-25290600	Weak transcription	Adipose Nuclei	Adipose
7	chr6:25281400-25292000	Weak transcription	Fetal Lung	lung
8	chr6:25281400-25295800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:25281400-25295800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:25281400-25295800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:25281400-25296000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:25281600-25290400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:25281600-25290600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:25281600-25290600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:25281600-25293800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:25281600-25293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:25281600-25294400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr6:25281600-25295600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:25281600-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:25281600-25295800	Weak transcription	Thymus	Thymus
21	chr6:25281600-25296000	Weak transcription	Primary T cells from cord blood	blood
22	chr6:25281600-25296000	Weak transcription	Fetal Thymus	thymus
23	chr6:25281600-25296400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:25281800-25290600	Weak transcription	Fetal Intestine Large	intestine
25	chr6:25281800-25291600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:25281800-25292400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:25281800-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:25282000-25292400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:25282200-25293800	Weak transcription	Lung	lung
30	chr6:25282800-25296400	Weak transcription	Hela-S3	cervix
31	chr6:25283600-25290400	Weak transcription	Left Ventricle	heart
32	chr6:25284600-25290600	Weak transcription	A549	lung
33	chr6:25285800-25290600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:25286400-25295000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:25286800-25300800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:25287600-25290600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:25287800-25296000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:25288000-25289400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr6:25288200-25289200	Enhancers	Fetal Heart	heart
40	chr6:25288400-25290200	Weak transcription	Aorta	Aorta
41	chr6:25288400-25290600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:25288400-25293600	Weak transcription	Fetal Intestine Small	intestine
43	chr6:25288600-25292200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:25288600-25292400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:25288600-25292600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:25288600-25295400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr6:25288600-25296000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:25288600-25296400	Weak transcription	Gastric	stomach
49	chr6:25288600-25301200	Weak transcription	Brain Anterior Caudate	brain
50	chr6:25288800-25291800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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