Variant report

Variant	rs1411453
Chromosome Location	chr9:117805764-117805765
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	chr1:164962387..164962927-chr9:117805695..117806490,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10817710	0.80[CEU][hapmap]
rs10982497	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10982503	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10982504	0.87[ASN][1000 genomes]
rs10982509	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982516	0.80[CEU][hapmap]
rs11788513	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12235159	0.80[CEU][hapmap]
rs12338715	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12340324	0.80[CEU][hapmap]
rs12343737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344929	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12346540	0.89[ASN][1000 genomes]
rs12347433	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12348090	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349585	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13285041	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13286217	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1411455	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2274751	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2274835	0.89[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2297179	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2297181	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28491824	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34865477	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789871	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3789875	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4394462	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs66539628	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7859478	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117781800-117808600	Weak transcription	Fetal Intestine Small	intestine
2	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
3	chr9:117789000-117808600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:117792800-117815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:117797400-117807400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
7	chr9:117799200-117819800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:117799400-117817000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:117800000-117806600	Strong transcription	NH-A	brain
10	chr9:117800600-117808600	Weak transcription	Fetal Intestine Large	intestine
11	chr9:117800800-117825000	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:117800800-117825200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:117801000-117812400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr9:117801000-117819200	Weak transcription	HMEC	breast
15	chr9:117801800-117820200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
17	chr9:117802400-117806000	Genic enhancers	Colon Smooth Muscle	Colon
18	chr9:117802600-117812400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:117803200-117808600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:117803400-117805800	Weak transcription	Fetal Stomach	stomach
21	chr9:117803400-117806200	Weak transcription	Fetal Lung	lung
22	chr9:117803400-117808400	Weak transcription	NHLF	lung
23	chr9:117803400-117810400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:117803400-117812000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:117803400-117820000	Weak transcription	Aorta	Aorta
26	chr9:117803400-117820600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:117803600-117806400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr9:117803600-117808200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:117803600-117820200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:117803600-117825400	Weak transcription	Fetal Kidney	kidney
31	chr9:117804200-117808200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:117804200-117808400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:117804600-117806800	Genic enhancers	Osteobl	bone
34	chr9:117804600-117807400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:117804600-117807600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:117804600-117808200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr9:117804600-117812800	Weak transcription	NHEK	skin
38	chr9:117804800-117806400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr9:117805000-117805800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:117805000-117805800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr9:117805000-117806000	Enhancers	Primary hematopoietic stem cells	blood
42	chr9:117805000-117806000	Enhancers	Adipose Nuclei	Adipose
43	chr9:117805000-117806000	Enhancers	HSMM	muscle
44	chr9:117805000-117806200	Enhancers	HSMMtube	muscle
45	chr9:117805000-117806200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
46	chr9:117805200-117805800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:117805200-117805800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:117805200-117806000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:117805200-117806000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:117805200-117806200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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