Variant report

Variant	rs2296668
Chromosome Location	chr9:95279588-95279589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95279396..95281425-chr9:95286686..95288458,2	K562	blood:
2	chr9:95245354..95247680-chr9:95279166..95281336,2	K562	blood:
3	chr9:95275292..95277875-chr9:95279129..95280868,3	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10115937	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10120210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10120292	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10435919	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1111047	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1536423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap]
rs2007245	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2131918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4744142	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6479427	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7043114	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7864757	0.81[EUR][1000 genomes]
rs7873646	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9886781	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9969804	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][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	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv1822933	chr9:95255176-95293308	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2296668	IPPK	cis	cerebellum	SCAN
rs2296668	ZNF484	cis	parietal	SCAN
rs2296668	CENPP	cis	parietal	SCAN
rs2296668	CENPP	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95269800-95298800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:95270400-95281000	Weak transcription	Thymus	Thymus
3	chr9:95270800-95284800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:95271200-95284800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:95271600-95285600	Weak transcription	Left Ventricle	heart
6	chr9:95274400-95281800	Strong transcription	Adipose Nuclei	Adipose
7	chr9:95275400-95279600	Weak transcription	Osteobl	bone
8	chr9:95275400-95282400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:95275600-95282200	Weak transcription	Fetal Stomach	stomach
10	chr9:95275800-95280000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:95275800-95285800	Weak transcription	Fetal Intestine Small	intestine
12	chr9:95276000-95281800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:95276000-95296600	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:95276800-95284000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:95278800-95280800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:95278800-95281400	Strong transcription	Liver	Liver
17	chr9:95279000-95280000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr9:95279000-95280200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:95279000-95280200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr9:95279000-95280600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr9:95279000-95280800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr9:95279000-95280800	Strong transcription	Aorta	Aorta
23	chr9:95279000-95282000	Strong transcription	Ovary	ovary
24	chr9:95279200-95279600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr9:95279200-95279600	Enhancers	H9 Cell Line	embryonic stem cell
26	chr9:95279200-95279600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:95279200-95279800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr9:95279200-95279800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr9:95279200-95280000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:95279200-95280200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:95279200-95280200	Enhancers	Gastric	stomach
32	chr9:95279200-95280800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr9:95279200-95283400	Strong transcription	Fetal Lung	lung
34	chr9:95279400-95279600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr9:95279400-95279600	Genic enhancers	Fetal Muscle Leg	muscle
36	chr9:95279400-95279600	Enhancers	Pancreas	Pancrea
37	chr9:95279400-95280200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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