Variant report

Variant	rs2975888
Chromosome Location	chr9:72727161-72727162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72611748..72614537-chr9:72726027..72728626,2	MCF-7	breast:
2	chr9:72726692..72728267-chr9:72871219..72873032,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10114529	1.00[AMR][1000 genomes]
rs10114669	1.00[AMR][1000 genomes]
rs12004563	1.00[AMR][1000 genomes]
rs12005951	1.00[AMR][1000 genomes]
rs12339185	1.00[AMR][1000 genomes]
rs12342376	1.00[AMR][1000 genomes]
rs12351302	1.00[AMR][1000 genomes]
rs28851550	1.00[AMR][1000 genomes]
rs2975892	1.00[AMR][1000 genomes]
rs2997707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2997708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2997709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2997710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2997711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2997712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2997713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3015216	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3015217	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3015219	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647410	1.00[AMR][1000 genomes]
rs73647413	1.00[AMR][1000 genomes]
rs752781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs752782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs752783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs752784	1.00[YRI][hapmap];0.96[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	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv949052	chr9:72698039-72741247	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72713800-72728200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:72714800-72742400	Weak transcription	Aorta	Aorta
3	chr9:72722000-72729600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:72722000-72758400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:72723200-72728400	Genic enhancers	Colon Smooth Muscle	Colon
6	chr9:72724200-72729200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:72724400-72742600	Weak transcription	Right Ventricle	heart
8	chr9:72725000-72727200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:72725000-72728800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:72725000-72728800	Genic enhancers	Stomach Smooth Muscle	stomach
11	chr9:72725200-72728600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:72725200-72728800	Enhancers	HMEC	breast
13	chr9:72725200-72735800	Weak transcription	Fetal Brain Male	brain
14	chr9:72725400-72728400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:72725600-72728800	Enhancers	Stomach Mucosa	stomach
16	chr9:72725600-72735400	Weak transcription	Right Atrium	heart
17	chr9:72725600-72740400	Weak transcription	Fetal Lung	lung
18	chr9:72725600-72745200	Weak transcription	Lung	lung
19	chr9:72725800-72728600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:72725800-72728800	Enhancers	HepG2	liver
21	chr9:72725800-72742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:72725800-72764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:72726000-72727200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:72726000-72727200	Enhancers	NH-A	brain
25	chr9:72726000-72727400	Strong transcription	HSMMtube	muscle
26	chr9:72726000-72727800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:72726000-72728000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:72726000-72728000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:72726000-72728000	Weak transcription	NHDF-Ad	bronchial
30	chr9:72726000-72728000	Weak transcription	NHLF	lung
31	chr9:72726000-72728200	Genic enhancers	HSMM	muscle
32	chr9:72726000-72728600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:72726000-72729200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr9:72726000-72729200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:72726000-72729600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:72726000-72729600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:72726000-72731400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr9:72726000-72734600	Weak transcription	Adipose Nuclei	Adipose
39	chr9:72726000-72735800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:72726200-72741000	Weak transcription	Fetal Stomach	stomach
41	chr9:72726200-72749200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr9:72726600-72728000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr9:72726600-72728800	Enhancers	NHEK	skin
44	chr9:72726600-72730000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:72726800-72727200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:72726800-72727200	Enhancers	Pancreas	Pancrea
47	chr9:72726800-72727200	Genic enhancers	Rectal Smooth Muscle	rectum
48	chr9:72726800-72727800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:72726800-72728000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr9:72726800-72728000	Weak transcription	Osteobl	bone

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