Variant report

Variant	rs2148861
Chromosome Location	chr9:72751276-72751277
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	chr9:72748535..72750686-chr9:72751248..72753868,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1007127	0.85[ASN][1000 genomes]
rs10119662	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10125617	0.82[JPT][hapmap]
rs10481740	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10481741	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10735583	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10780811	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868720	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs10868799	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs10868801	0.83[JPT][hapmap]
rs11142350	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs1536956	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs1927106	0.94[ASN][1000 genomes]
rs1927115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927128	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1927139	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2026136	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs2182739	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs2209779	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2281935	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2309611	0.95[CEU][hapmap]
rs2309633	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2309642	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2975862	0.90[ASN][1000 genomes]
rs2975890	0.94[ASN][1000 genomes]
rs2975907	0.88[ASN][1000 genomes]
rs2975908	0.86[ASN][1000 genomes]
rs2975910	0.87[ASN][1000 genomes]
rs2975915	0.86[ASN][1000 genomes]
rs2975917	0.86[ASN][1000 genomes]
rs2997652	0.81[ASN][1000 genomes]
rs2997664	0.86[ASN][1000 genomes]
rs2997676	0.87[ASN][1000 genomes]
rs2997677	0.87[ASN][1000 genomes]
rs2997678	0.87[ASN][1000 genomes]
rs3015168	0.87[ASN][1000 genomes]
rs3015224	0.89[ASN][1000 genomes]
rs3015232	0.85[ASN][1000 genomes]
rs3015238	0.86[ASN][1000 genomes]
rs3015242	0.86[ASN][1000 genomes]
rs4375070	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs4744968	0.85[ASN][1000 genomes]
rs4744977	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744978	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4745000	0.82[JPT][hapmap]
rs6560019	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7027209	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS 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 target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72722000-72758400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:72725800-72764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:72726800-72785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:72727000-72776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:72728200-72752800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:72728200-72758400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr9:72731200-72768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:72736200-72761200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:72740600-72766400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:72741000-72758600	Weak transcription	Colonic Mucosa	Colon
11	chr9:72741400-72765600	Weak transcription	Esophagus	oesophagus
12	chr9:72741600-72751600	Weak transcription	NHLF	lung
13	chr9:72741600-72755000	Weak transcription	Left Ventricle	heart
14	chr9:72741600-72757400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:72741600-72775400	Weak transcription	Adipose Nuclei	Adipose
16	chr9:72741600-72789400	Weak transcription	Spleen	Spleen
17	chr9:72743000-72754800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:72746200-72755000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:72746600-72762600	Weak transcription	Psoas Muscle	Psoas
20	chr9:72747400-72752600	Enhancers	HSMM	muscle
21	chr9:72747800-72753400	Enhancers	NHDF-Ad	bronchial
22	chr9:72748000-72751400	Enhancers	Osteobl	bone
23	chr9:72748000-72752800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:72748200-72751600	Genic enhancers	HSMMtube	muscle
25	chr9:72748200-72752000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:72748200-72752800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:72748400-72753800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr9:72748600-72762000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:72748800-72751600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:72749400-72758400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:72749600-72755000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:72749800-72752000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr9:72749800-72762600	Weak transcription	Fetal Stomach	stomach
34	chr9:72749800-72763000	Weak transcription	Lung	lung
35	chr9:72750000-72752400	Enhancers	HUVEC	blood vessel
36	chr9:72750000-72752600	Enhancers	NH-A	brain
37	chr9:72750200-72752600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:72750200-72753000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:72750200-72753000	Enhancers	NHEK	skin
40	chr9:72750200-72753200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:72750200-72753800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:72750400-72752400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:72750400-72762600	Weak transcription	Fetal Muscle Leg	muscle
44	chr9:72750400-72771600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:72750600-72752800	Enhancers	HMEC	breast
46	chr9:72750600-72754800	Weak transcription	Colon Smooth Muscle	Colon
47	chr9:72750800-72758400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:72751000-72757000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:72751000-72771800	Weak transcription	Aorta	Aorta
50	chr9:72751200-72752400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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