Variant report

Variant	rs2647471
Chromosome Location	chr1:220255032-220255033
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220253135..220256088-chr1:220267328..220268920,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067704	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11118488	1.00[MEX][hapmap]
rs11800305	1.00[MEX][hapmap]
rs11807333	1.00[MEX][hapmap]
rs1611863	0.80[AFR][1000 genomes]
rs2577135	0.83[AFR][1000 genomes]
rs2577153	1.00[AMR][1000 genomes]
rs2647472	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes]
rs2789785	1.00[ASW][hapmap];0.86[LWK][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs2889877	1.00[MEX][hapmap]
rs7524161	0.83[AFR][1000 genomes]
rs904327	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220220400-220257600	Weak transcription	Stomach Mucosa	stomach
2	chr1:220220600-220262400	Weak transcription	Pancreas	Pancrea
3	chr1:220220600-220262400	Weak transcription	NHLF	lung
4	chr1:220220800-220261600	Weak transcription	Fetal Brain Male	brain
5	chr1:220236400-220262800	Weak transcription	Esophagus	oesophagus
6	chr1:220238000-220262800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:220238000-220267400	Weak transcription	Spleen	Spleen
8	chr1:220238200-220262800	Weak transcription	Gastric	stomach
9	chr1:220239400-220262000	Weak transcription	Brain Germinal Matrix	brain
10	chr1:220239600-220255200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:220239600-220261600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:220239600-220262400	Weak transcription	Right Ventricle	heart
13	chr1:220241200-220256800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:220241200-220258200	Weak transcription	Hela-S3	cervix
15	chr1:220241200-220261800	Weak transcription	A549	lung
16	chr1:220241200-220262000	Weak transcription	HMEC	breast
17	chr1:220241200-220262400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:220241200-220262400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:220241400-220262400	Weak transcription	NHEK	skin
20	chr1:220242600-220262800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:220243800-220262400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:220246200-220262000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:220246400-220256000	Weak transcription	Fetal Kidney	kidney
24	chr1:220246400-220261600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:220246400-220261800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:220246400-220262000	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:220246400-220262400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:220246400-220262400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:220246400-220262400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:220246400-220262400	Weak transcription	Brain Anterior Caudate	brain
31	chr1:220246400-220262400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:220246400-220262400	Weak transcription	Brain Substantia Nigra	brain
33	chr1:220246400-220262400	Weak transcription	Fetal Brain Female	brain
34	chr1:220246600-220262400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:220246600-220262400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:220246600-220262400	Weak transcription	Colonic Mucosa	Colon
37	chr1:220246800-220262400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:220246800-220262400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:220246800-220262400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:220246800-220262400	Weak transcription	Fetal Heart	heart
41	chr1:220246800-220262400	Weak transcription	Thymus	Thymus
42	chr1:220247000-220256800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:220247000-220257600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:220247000-220258600	Weak transcription	Ovary	ovary
45	chr1:220247000-220262400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:220247000-220262400	Weak transcription	Aorta	Aorta
47	chr1:220247000-220262400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:220247000-220262400	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:220247000-220262800	Weak transcription	Lung	lung
50	chr1:220247200-220262400	Weak transcription	Adipose Nuclei	Adipose

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