Variant report

Variant	rs16906859
Chromosome Location	chr9:93591865-93591866
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	chr9:93563668..93565517-chr9:93590298..93592693,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10993696	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs10993697	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10993698	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10993708	1.00[CEU][hapmap]
rs10993710	1.00[CEU][hapmap]
rs10993714	1.00[CEU][hapmap]
rs10993715	1.00[CEU][hapmap]
rs10993717	1.00[CEU][hapmap]
rs10993718	1.00[CEU][hapmap]
rs11788207	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs12237702	1.00[CEU][hapmap]
rs12551275	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs12553524	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1460834	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs1460835	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs16906825	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17488335	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs2042983	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2042984	1.00[CHB][hapmap]
rs2115484	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2115485	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2126051	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs290233	0.92[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs290240	0.85[CHB][hapmap]
rs290241	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3789891	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs3789892	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs3789893	0.85[ASN][1000 genomes]
rs4002566	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61495376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7020331	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs7032733	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7046173	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs7046193	0.92[CHB][hapmap]
rs7046316	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs72729008	0.85[ASN][1000 genomes]
rs72729009	0.85[ASN][1000 genomes]
rs72729010	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72729013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72729020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72729022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72729024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742789	1.00[AFR][1000 genomes]
rs72746350	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893567	chr9:93519280-93609668	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:93567800-93597400	Weak transcription	Gastric	stomach
3	chr9:93577000-93598800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:93577800-93606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:93578600-93592400	Weak transcription	Esophagus	oesophagus
6	chr9:93580800-93603400	Weak transcription	K562	blood
7	chr9:93581200-93593400	Weak transcription	Stomach Mucosa	stomach
8	chr9:93582600-93595200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:93583000-93599600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:93585400-93593200	Weak transcription	Fetal Intestine Small	intestine
11	chr9:93585400-93594600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:93585400-93594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:93585600-93607800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:93589200-93592200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr9:93589200-93592400	Weak transcription	Spleen	Spleen
16	chr9:93589200-93606000	Weak transcription	Colonic Mucosa	Colon
17	chr9:93589600-93592600	Weak transcription	Thymus	Thymus
18	chr9:93589800-93592400	Weak transcription	Fetal Stomach	stomach
19	chr9:93590000-93593200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:93590000-93601600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:93590400-93593600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr9:93591000-93599600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:93591000-93603200	Weak transcription	Fetal Kidney	kidney
24	chr9:93591200-93592200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:93591200-93592400	Weak transcription	Fetal Thymus	thymus
26	chr9:93591200-93592400	Weak transcription	Lung	lung
27	chr9:93591200-93592400	Weak transcription	Pancreas	Pancrea
28	chr9:93591200-93592600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr9:93591200-93593600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr9:93591200-93595000	Weak transcription	Adipose Nuclei	Adipose
31	chr9:93591200-93596400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:93591400-93595000	Weak transcription	Small Intestine	intestine
33	chr9:93591600-93592800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:93591600-93592800	Flanking Active TSS	GM12878-XiMat	blood
35	chr9:93591800-93592000	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
36	chr9:93591800-93592000	Enhancers	Primary hematopoietic stem cells	blood
37	chr9:93591800-93592000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr9:93591800-93592600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:93591800-93596400	Strong transcription	Monocytes-CD14+_RO01746	blood

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