Variant report

Variant	rs7875681
Chromosome Location	chr9:95245243-95245244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95245180..95247895-chr9:95248279..95250997,3	K562	blood:
2	chr9:95238409..95241163-chr9:95245198..95246884,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10115976	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10117603	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119535	0.90[ASN][1000 genomes]
rs10156530	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10283718	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820962	0.90[ASN][1000 genomes]
rs10820963	0.90[ASN][1000 genomes]
rs10820970	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820973	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820982	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10820995	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10992308	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992312	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992314	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10992334	0.90[ASN][1000 genomes]
rs10992348	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992350	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992359	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12347857	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349712	0.90[ASN][1000 genomes]
rs12350198	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12350842	1.00[CEU][hapmap]
rs12352447	0.90[ASN][1000 genomes]
rs12378023	0.86[EUR][1000 genomes]
rs1447114	0.90[ASN][1000 genomes]
rs1951849	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744140	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56168105	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58391046	0.90[ASN][1000 genomes]
rs6479425	0.86[EUR][1000 genomes]
rs7027998	0.92[EUR][1000 genomes]
rs7036078	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7036459	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7037068	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7860297	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7862677	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7872739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7873882	0.94[CEU][hapmap];0.90[ASN][1000 genomes]
rs9695754	0.94[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][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	nsv1049599	chr9:95170139-95265558	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7875681	CENPP	cis	Thyroid	GTEx
rs7875681	CENPP	cis	Nerve Tibial	GTEx
rs7875681	CENPP	cis	Esophagus Muscularis	GTEx
rs7875681	ZNF484	cis	parietal	SCAN
rs7875681	CENPP	cis	Artery Tibial	GTEx
rs7875681	CENPP	cis	cerebellum	SCAN
rs7875681	CENPP	cis	Artery Aorta	GTEx
rs7875681	CENPP	cis	Adipose Subcutaneous	GTEx
rs7875681	CENPP	cis	Muscle Skeletal	GTEx
rs7875681	CENPP	cis	parietal	SCAN
rs7875681	CENPP	cis	lung	GTEx
rs7875681	NOL8	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95231800-95268800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:95235400-95251600	Weak transcription	Psoas Muscle	Psoas
3	chr9:95241200-95246800	Enhancers	Fetal Lung	lung
4	chr9:95241400-95251800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:95241400-95255000	Weak transcription	Esophagus	oesophagus
6	chr9:95241600-95245600	Weak transcription	Lung	lung
7	chr9:95242600-95247200	Enhancers	NHDF-Ad	bronchial
8	chr9:95242800-95247200	Weak transcription	Left Ventricle	heart
9	chr9:95243000-95248200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:95243400-95245800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:95243400-95246000	Weak transcription	Right Ventricle	heart
12	chr9:95243600-95245800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:95243600-95246000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:95243600-95251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:95243600-95263800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:95243800-95245800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr9:95243800-95245800	Weak transcription	Hela-S3	cervix
18	chr9:95243800-95246000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:95243800-95246600	Enhancers	NHEK	skin
20	chr9:95243800-95248400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:95243800-95248400	Weak transcription	K562	blood
22	chr9:95243800-95251200	Weak transcription	HSMM	muscle
23	chr9:95243800-95251200	Weak transcription	HSMMtube	muscle
24	chr9:95243800-95251400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:95243800-95251400	Weak transcription	Aorta	Aorta
26	chr9:95244000-95245400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:95244000-95245800	Weak transcription	Right Atrium	heart
28	chr9:95244000-95246000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:95244000-95246000	Weak transcription	HMEC	breast
30	chr9:95244000-95246000	Weak transcription	HUVEC	blood vessel
31	chr9:95244000-95246000	Weak transcription	NH-A	brain
32	chr9:95244400-95247400	Enhancers	Fetal Heart	heart
33	chr9:95244600-95247400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:95244800-95245800	Weak transcription	Adipose Nuclei	Adipose
35	chr9:95244800-95245800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr9:95244800-95246000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:95244800-95246000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:95244800-95246000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:95244800-95247000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:95244800-95247200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:95244800-95247400	Enhancers	Fetal Stomach	stomach
42	chr9:95245000-95246200	Enhancers	Fetal Muscle Leg	muscle
43	chr9:95245000-95246800	Enhancers	Colon Smooth Muscle	Colon
44	chr9:95245000-95247200	Enhancers	Rectal Smooth Muscle	rectum
45	chr9:95245000-95247200	Enhancers	NHLF	lung
46	chr9:95245000-95247400	Enhancers	Stomach Smooth Muscle	stomach
47	chr9:95245200-95245400	Enhancers	Duodenum Mucosa	Duodenum
48	chr9:95245200-95245400	Enhancers	Fetal Intestine Small	intestine
49	chr9:95245200-95245800	Weak transcription	Osteobl	bone
50	chr9:95245200-95247200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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