Variant report

Variant	rs2744269
Chromosome Location	chr6:25280677-25280678
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	chr6:25201388..25203909-chr6:25279159..25280911,2	MCF-7	breast:
2	chr6:25277929..25281528-chr6:25281560..25287992,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264238	Chromatin interaction
ENSG00000207286	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1016855	0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2064211	0.81[CEU][hapmap]
rs2690054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690061	0.88[EUR][1000 genomes]
rs2690064	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2690067	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2744254	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2744257	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2744258	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2744267	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2744268	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2744300	0.82[JPT][hapmap]
rs6908902	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909014	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914799	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6926126	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721036	0.81[CEU][hapmap]
rs721037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723048	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73392379	0.87[AFR][1000 genomes]
rs9358848	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9358849	0.84[CEU][hapmap]
rs9366614	0.81[CEU][hapmap]
rs9379746	0.81[CEU][hapmap]
rs9379747	0.81[CEU][hapmap]
rs9393635	0.90[EUR][1000 genomes]
rs9393637	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	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
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25278400-25280800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25278400-25281600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:25278400-25281600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:25278400-25281600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:25278600-25281000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:25278600-25281000	Active TSS	A549	lung
7	chr6:25278600-25281200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:25278600-25281400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr6:25278600-25281400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr6:25278600-25281400	Active TSS	Right Ventricle	heart
11	chr6:25278600-25283400	Active TSS	Aorta	Aorta
12	chr6:25278800-25280800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:25278800-25280800	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr6:25278800-25281000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:25278800-25281000	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:25278800-25281000	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr6:25278800-25281000	Active TSS	Placenta Amnion	Placenta Amnion
18	chr6:25278800-25281200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:25278800-25281200	Active TSS	Esophagus	oesophagus
20	chr6:25278800-25281200	Active TSS	Ovary	ovary
21	chr6:25278800-25281400	Active TSS	Fetal Kidney	kidney
22	chr6:25278800-25281600	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr6:25278800-25281600	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr6:25278800-25281600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:25278800-25281600	Active TSS	Right Atrium	heart
26	chr6:25279000-25280800	Active TSS	Colon Smooth Muscle	Colon
27	chr6:25279000-25280800	Active TSS	Fetal Lung	lung
28	chr6:25279000-25280800	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr6:25279000-25280800	Active TSS	Hela-S3	cervix
30	chr6:25279000-25280800	Active TSS	HSMM	muscle
31	chr6:25279000-25281000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:25279000-25281000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:25279000-25281000	Active TSS	Pancreas	Pancrea
34	chr6:25279000-25281000	Active TSS	Small Intestine	intestine
35	chr6:25279000-25281000	Active TSS	NHDF-Ad	bronchial
36	chr6:25279000-25281200	Active TSS	Gastric	stomach
37	chr6:25279000-25281400	Active TSS	Fetal Intestine Small	intestine
38	chr6:25279000-25281400	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr6:25279000-25281600	Active TSS	H1 Cell Line	embryonic stem cell
40	chr6:25279000-25281600	Active TSS	Left Ventricle	heart
41	chr6:25279000-25281800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:25279000-25281800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:25279000-25281800	Active TSS	Fetal Intestine Large	intestine
44	chr6:25279200-25280800	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr6:25279200-25280800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:25279200-25280800	Active TSS	Thymus	Thymus
47	chr6:25279200-25280800	Active TSS	NHEK	skin
48	chr6:25279200-25281000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr6:25279200-25281600	Active TSS	Brain Cingulate Gyrus	brain
50	chr6:25279200-25281600	Active TSS	NHLF	lung

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