Variant report

Variant	rs9987000
Chromosome Location	chr7:25883207-25883208
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	chr7:25878574..25880347-chr7:25882130..25884614,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10232819	0.93[ASN][1000 genomes]
rs10238703	0.94[EUR][1000 genomes]
rs10241634	0.94[EUR][1000 genomes]
rs10242536	0.95[EUR][1000 genomes]
rs10245353	0.91[EUR][1000 genomes]
rs10260677	0.94[EUR][1000 genomes]
rs10261019	0.84[ASN][1000 genomes]
rs10262483	0.97[EUR][1000 genomes]
rs10267498	0.93[EUR][1000 genomes]
rs10282436	0.95[EUR][1000 genomes]
rs1055144	0.95[EUR][1000 genomes]
rs10951112	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770186	1.00[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs11976790	0.93[ASN][1000 genomes]
rs12666961	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12700667	0.85[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.88[ASN][1000 genomes]
rs1376527	0.93[ASN][1000 genomes]
rs1451383	0.87[ASN][1000 genomes]
rs1451385	0.83[CEU][hapmap];0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs2391168	0.94[EUR][1000 genomes]
rs28392961	0.88[EUR][1000 genomes]
rs28473292	0.95[EUR][1000 genomes]
rs28858973	0.94[EUR][1000 genomes]
rs2893221	0.95[EUR][1000 genomes]
rs35766302	0.97[EUR][1000 genomes]
rs4141278	0.89[EUR][1000 genomes]
rs41469349	0.95[EUR][1000 genomes]
rs4722528	0.84[ASN][1000 genomes]
rs4722529	0.91[ASN][1000 genomes]
rs4722530	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722531	0.93[ASN][1000 genomes]
rs57246313	0.92[EUR][1000 genomes]
rs6461887	0.93[ASN][1000 genomes]
rs6958350	0.93[ASN][1000 genomes]
rs7793216	0.93[ASN][1000 genomes]
rs7798002	0.92[EUR][1000 genomes]
rs7798130	0.94[EUR][1000 genomes]
rs979165	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830928	chr7:25820147-25965014	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9987000	SKAP2	cis	cerebellum	SCAN
rs9987000	CCDC126	cis	parietal	SCAN
rs9987000	TRIL	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25871200-25885400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:25872200-25886200	Weak transcription	NHLF	lung
3	chr7:25872400-25885200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr7:25876800-25885000	Weak transcription	Fetal Kidney	kidney
5	chr7:25879200-25884200	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr7:25880000-25888800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:25880000-25889000	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr7:25880200-25883400	Enhancers	Left Ventricle	heart
9	chr7:25880400-25883800	Weak transcription	Aorta	Aorta
10	chr7:25880400-25885200	Weak transcription	Ovary	ovary
11	chr7:25881000-25884000	Enhancers	Fetal Muscle Leg	muscle
12	chr7:25881400-25883800	Enhancers	Colon Smooth Muscle	Colon
13	chr7:25881600-25883400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:25881800-25883400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr7:25881800-25884000	Enhancers	Right Atrium	heart
16	chr7:25881800-25889000	Enhancers	Osteobl	bone
17	chr7:25882000-25885400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:25882200-25883800	Weak transcription	NH-A	brain
19	chr7:25882200-25884600	Weak transcription	Fetal Stomach	stomach
20	chr7:25882200-25885600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:25882200-25892000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:25882400-25883600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:25882400-25884800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr7:25882600-25883400	Enhancers	Fetal Muscle Trunk	muscle
25	chr7:25882600-25883400	Enhancers	Right Ventricle	heart
26	chr7:25882600-25885600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:25882800-25883800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:25882800-25883800	Weak transcription	Fetal Lung	lung
29	chr7:25882800-25885200	Weak transcription	Adipose Nuclei	Adipose
30	chr7:25882800-25885400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:25882800-25886600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:25883000-25883400	Weak transcription	Fetal Heart	heart
33	chr7:25883000-25883400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr7:25883000-25885400	Weak transcription	Psoas Muscle	Psoas
35	chr7:25883000-25887000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr7:25883200-25883400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:25883200-25884200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr7:25883200-25887200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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