Variant report

Variant	rs290247
Chromosome Location	chr9:93583969-93583970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1081767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1172681	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];0.99[ASN][1000 genomes]
rs167078	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];0.99[ASN][1000 genomes]
rs169724	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs182361	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs187306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs188312	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013826	0.86[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs290211	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs290212	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs290214	0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs290215	0.90[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs290216	0.92[ASN][1000 genomes]
rs290217	0.94[ASN][1000 genomes]
rs290218	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs290219	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs290245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290248	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290250	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs290251	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290252	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs290974	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs290975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs290976	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];0.99[ASN][1000 genomes]
rs290984	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290986	0.80[CHB][hapmap];0.84[MEX][hapmap]
rs4744505	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs745743	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs772410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs913980	0.90[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv893569	chr9:93552550-93587089	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	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:37 , 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	chr9:93567800-93584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:93567800-93584800	Weak transcription	Fetal Intestine Large	intestine
4	chr9:93567800-93597400	Weak transcription	Gastric	stomach
5	chr9:93572600-93591000	Weak transcription	Lung	lung
6	chr9:93572800-93584800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr9:93573200-93589600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:93577000-93585800	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr9:93577000-93598800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:93577200-93589000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:93577800-93584000	Weak transcription	HMEC	breast
12	chr9:93577800-93584800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr9:93577800-93585000	Weak transcription	Spleen	Spleen
14	chr9:93577800-93606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:93578000-93585000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:93578200-93585000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:93578600-93584800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:93578600-93592400	Weak transcription	Esophagus	oesophagus
19	chr9:93580400-93586600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr9:93580800-93588800	Weak transcription	Fetal Stomach	stomach
21	chr9:93580800-93603400	Weak transcription	K562	blood
22	chr9:93581200-93584000	Weak transcription	Thymus	Thymus
23	chr9:93581200-93584200	Weak transcription	Fetal Intestine Small	intestine
24	chr9:93581200-93593400	Weak transcription	Stomach Mucosa	stomach
25	chr9:93581400-93586800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:93581600-93585600	Weak transcription	Fetal Kidney	kidney
27	chr9:93581600-93585800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr9:93582600-93595200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:93582800-93584000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr9:93582800-93584600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:93583000-93584200	Weak transcription	Fetal Thymus	thymus
32	chr9:93583000-93584800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:93583000-93585600	Genic enhancers	Monocytes-CD14+_RO01746	blood
34	chr9:93583000-93599600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:93583200-93584000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:93583600-93584000	Genic enhancers	Primary B cells from cord blood	blood
37	chr9:93583600-93584200	Enhancers	Primary neutrophils fromperipheralblood	blood

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