Variant report

Variant	rs6469789
Chromosome Location	chr8:119960661-119960662
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:119954185..119957500-chr8:119957720..119961384,3	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10101385	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10505348	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10955908	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10955915	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11573824	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11573829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573885	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11992136	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs13250753	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13254554	0.80[ASN][1000 genomes]
rs13264791	0.84[EUR][1000 genomes]
rs13277230	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13439134	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1485289	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1872426	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1905786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1982763	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2062375	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2062377	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2073617	0.81[EUR][1000 genomes]
rs2073618	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2220189	0.80[ASN][1000 genomes]
rs2450083	0.81[CEU][hapmap]
rs3102732	0.82[EUR][1000 genomes]
rs3134063	0.82[EUR][1000 genomes]
rs3134065	0.82[EUR][1000 genomes]
rs4242592	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4319131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4355801	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4407910	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4563920	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4567065	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4618726	0.80[ASN][1000 genomes]
rs4876869	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4876876	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6415470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6469788	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6992497	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7006553	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7010043	0.80[ASN][1000 genomes]
rs7010267	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7014574	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72680380	0.90[ASN][1000 genomes]
rs7463176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7464496	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7842942	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9969672	1.00[CHB][hapmap];0.94[JPT][hapmap]

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	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758169	chr8:119943309-120275750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2759639	chr8:119943309-120275750	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6469789	TNFRSF11B	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119945400-119960800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr8:119953400-119963600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:119954200-119962600	Weak transcription	Fetal Intestine Large	intestine
4	chr8:119959200-119961800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr8:119959400-119961600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr8:119959600-119960800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
7	chr8:119959600-119961600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr8:119959600-119961600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr8:119959600-119961600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:119959600-119961600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr8:119959600-119961600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr8:119959600-119961800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:119959600-119961800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr8:119959800-119961200	Active TSS	NHLF	lung
15	chr8:119960200-119961000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr8:119960200-119961600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr8:119960400-119960800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:119960400-119961000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr8:119960400-119961000	Flanking Active TSS	Fetal Lung	lung
20	chr8:119960400-119961000	Transcr. at gene 5' and 3'	Osteobl	bone
21	chr8:119960400-119961200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr8:119960400-119961600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr8:119960400-119961800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:119960400-119962200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr8:119960400-119962200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr8:119960400-119962600	Active TSS	Fetal Kidney	kidney
27	chr8:119960600-119960800	Enhancers	Brain Anterior Caudate	brain
28	chr8:119960600-119960800	Enhancers	Fetal Brain Male	brain
29	chr8:119960600-119960800	Flanking Active TSS	HSMMtube	muscle
30	chr8:119960600-119961000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr8:119960600-119961000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:119960600-119961000	Enhancers	H9 Cell Line	embryonic stem cell
33	chr8:119960600-119961000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr8:119960600-119961000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr8:119960600-119961200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr8:119960600-119961200	Enhancers	Fetal Brain Female	brain
37	chr8:119960600-119961200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr8:119960600-119961400	Enhancers	Adipose Nuclei	Adipose
39	chr8:119960600-119962000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr8:119960600-119963800	Active TSS	Right Ventricle	heart
41	chr8:119960600-119964800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr8:119960600-119965000	Active TSS	Aorta	Aorta

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