Variant report

Variant	rs700809
Chromosome Location	chr9:79240050-79240051
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	chr9:79234093..79236437-chr9:79239287..79241420,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10512062	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1329020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1425286	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1536821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700803	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs700804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042069	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7046144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs707741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79224600-79244400	Weak transcription	Brain Angular Gyrus	brain
2	chr9:79225400-79244000	Weak transcription	Brain Hippocampus Middle	brain
3	chr9:79225400-79265600	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:79230200-79248200	Weak transcription	Fetal Stomach	stomach
5	chr9:79230400-79241200	Enhancers	Fetal Intestine Large	intestine
6	chr9:79230600-79241400	Weak transcription	Primary B cells from cord blood	blood
7	chr9:79232800-79261400	Weak transcription	Colonic Mucosa	Colon
8	chr9:79234000-79246000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:79234200-79246000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:79234200-79252200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr9:79234400-79257800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:79234400-79259600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:79234600-79249200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:79235200-79240600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:79236000-79245800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:79236000-79249200	Weak transcription	NHDF-Ad	bronchial
17	chr9:79236000-79257000	Weak transcription	Osteobl	bone
18	chr9:79236200-79248800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:79236200-79252400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:79236200-79257400	Weak transcription	Adipose Nuclei	Adipose
21	chr9:79236200-79257600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:79236400-79243800	Weak transcription	Fetal Thymus	thymus
23	chr9:79236600-79240600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:79236600-79241200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:79236600-79241400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:79236600-79249000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:79236800-79241400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr9:79238400-79240200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:79238400-79240400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:79238400-79240400	Enhancers	Fetal Brain Male	brain
31	chr9:79238400-79241400	Enhancers	Fetal Intestine Small	intestine
32	chr9:79238600-79248400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:79238600-79261200	Strong transcription	HSMM	muscle
34	chr9:79238800-79240600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:79238800-79241000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr9:79239000-79240400	Strong transcription	Aorta	Aorta
37	chr9:79239000-79240400	Strong transcription	Brain Anterior Caudate	brain
38	chr9:79239000-79241800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:79239000-79241800	Enhancers	Duodenum Mucosa	Duodenum
40	chr9:79239000-79244600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:79239200-79240200	Flanking Active TSS	GM12878-XiMat	blood
42	chr9:79239200-79241600	Strong transcription	Colon Smooth Muscle	Colon
43	chr9:79239200-79242400	Enhancers	Stomach Mucosa	stomach
44	chr9:79239200-79242600	Strong transcription	HSMMtube	muscle
45	chr9:79239400-79240400	Enhancers	Small Intestine	intestine
46	chr9:79239600-79240400	Strong transcription	Brain Cingulate Gyrus	brain
47	chr9:79239600-79240400	Strong transcription	Brain Substantia Nigra	brain
48	chr9:79239600-79240600	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr9:79239600-79244600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:79239600-79254400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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