Variant report

Variant	rs2290887
Chromosome Location	chr9:93640009-93640010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:93638591..93640127-chr9:93644373..93647334,2	K562	blood:
2	chr9:93633763..93637108-chr9:93639159..93643075,3	MCF-7	breast:
3	chr9:93563257..93565771-chr9:93639113..93640661,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10124093	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs10512203	1.00[GIH][hapmap]
rs10993725	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs10993727	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs10993728	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10993729	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12001366	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs12003597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003608	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005209	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005550	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12006330	1.00[GIH][hapmap]
rs12686497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12686499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16906904	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16906923	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290886	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290888	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290891	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306039	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2306041	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34872092	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36063880	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3789903	0.92[GIH][hapmap]
rs3789905	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827824	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529574	0.86[CEU][hapmap];0.84[CHD][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4744018	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744516	0.88[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs4744517	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4744518	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55804113	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020271	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71494431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71494432	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7846754	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7846869	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872076	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	nsv1039761	chr9:93598856-93677831	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv430078	chr9:93609668-93642766	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1053252	chr9:93610132-93699103	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv430079	chr9:93620963-93642766	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv416495	chr9:93638584-93643961	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv416141	chr9:93638589-93643961	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2290887	CENPP	cis	parietal	SCAN
rs2290887	NFIL3	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93601800-93642200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:93611200-93642200	Weak transcription	Stomach Mucosa	stomach
3	chr9:93617200-93640600	Weak transcription	K562	blood
4	chr9:93617400-93640600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:93617800-93640600	Weak transcription	NHEK	skin
6	chr9:93623600-93642400	Weak transcription	Adipose Nuclei	Adipose
7	chr9:93625000-93642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:93625200-93642400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:93626000-93647800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:93629200-93640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:93630000-93644800	Weak transcription	Pancreas	Pancrea
12	chr9:93632600-93641600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr9:93633400-93645800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:93633800-93645400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:93634000-93642600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:93634000-93645800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr9:93634000-93646200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:93634000-93646400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:93634000-93666200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr9:93634400-93646600	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr9:93635200-93640800	Strong transcription	Fetal Intestine Small	intestine
22	chr9:93635600-93646200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr9:93636000-93644000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:93636400-93650600	Weak transcription	Liver	Liver
25	chr9:93637000-93640800	Weak transcription	Fetal Kidney	kidney
26	chr9:93637200-93640400	Weak transcription	GM12878-XiMat	blood
27	chr9:93637200-93642400	Weak transcription	Lung	lung
28	chr9:93637200-93642400	Weak transcription	Small Intestine	intestine
29	chr9:93638200-93641800	Strong transcription	Primary B cells from cord blood	blood
30	chr9:93638800-93646800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr9:93639400-93640200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:93639400-93640200	Strong transcription	Colonic Mucosa	Colon
33	chr9:93639400-93642800	Strong transcription	Spleen	Spleen
34	chr9:93639400-93643400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:93639400-93643600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:93639400-93643600	Strong transcription	Gastric	stomach
37	chr9:93639400-93645600	Strong transcription	Thymus	Thymus
38	chr9:93639400-93645800	Strong transcription	Fetal Thymus	thymus
39	chr9:93639400-93646200	Strong transcription	Fetal Stomach	stomach
40	chr9:93639400-93646400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:93639400-93647000	Weak transcription	HMEC	breast
42	chr9:93639600-93640600	Strong transcription	Esophagus	oesophagus
43	chr9:93639800-93643400	Strong transcription	Fetal Intestine Large	intestine
44	chr9:93640000-93641000	Enhancers	Placenta Amnion	Placenta Amnion
45	chr9:93640000-93646400	Strong transcription	Primary hematopoietic stem cells	blood

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