Variant report

Variant	rs2518116
Chromosome Location	chr9:108320988-108320989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr9:108319844-108321105	A549	lung:	n/a	n/a
2	NR2F2	chr9:108320096-108321030	MCF-7	breast:	n/a	n/a
3	MXI1	chr9:108319766-108321358	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr9:108319985-108321126	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr9:108319888-108321156	HepG2	liver:	n/a	n/a
6	MAX	chr9:108320122-108321029	SK-N-SH	brain:	n/a	n/a
7	E2F6	chr9:108320059-108321104	A549	lung:	n/a	n/a
8	POLR2A	chr9:108319746-108321517	GM12891	blood:	n/a	n/a
9	MAX	chr9:108319917-108320996	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000228317	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10761100	0.99[ASN][1000 genomes]
rs10816278	0.86[ASN][1000 genomes]
rs10816284	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs10820810	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10820812	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820813	0.84[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12686557	0.86[AMR][1000 genomes]
rs1327354	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1360089	0.92[ASN][1000 genomes]
rs1806898	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1815383	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1960023	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1987634	0.94[ASN][1000 genomes]
rs2225246	0.89[ASN][1000 genomes]
rs2427769	0.96[ASN][1000 genomes]
rs2518106	0.80[JPT][hapmap]
rs2518112	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2518114	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2518120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2518123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2518124	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2518128	0.80[JPT][hapmap]
rs2768279	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2768283	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2768290	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2768291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2768292	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2768294	0.80[JPT][hapmap]
rs2771038	0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2771041	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2771042	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2812297	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs2812303	0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2812307	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2812308	0.91[ASN][1000 genomes]
rs2812310	0.94[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs4742650	0.84[ASN][1000 genomes]
rs4742947	0.89[ASN][1000 genomes]
rs4742948	0.99[ASN][1000 genomes]
rs6477447	0.82[ASN][1000 genomes]
rs6477449	0.98[ASN][1000 genomes]
rs7020083	0.89[ASN][1000 genomes]
rs7357632	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7357782	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7864020	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv1049133	chr9:108292302-108356068	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2518116	PPP3R2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108319400-108321000	Active TSS	GM12878-XiMat	blood
2	chr9:108319600-108321200	Active TSS	Right Atrium	heart
3	chr9:108319800-108321000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:108319800-108321000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:108319800-108321000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:108319800-108321000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:108319800-108321000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr9:108319800-108321000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr9:108319800-108321000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr9:108319800-108321000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:108319800-108321000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:108319800-108321000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:108319800-108321000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr9:108319800-108321000	Active TSS	Primary T cells from cord blood	blood
15	chr9:108319800-108321000	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr9:108319800-108321000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:108319800-108321000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:108319800-108321000	Active TSS	Muscle Satellite Cultured Cells	--
19	chr9:108319800-108321000	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr9:108319800-108321000	Active TSS	Aorta	Aorta
21	chr9:108319800-108321000	Active TSS	Brain Angular Gyrus	brain
22	chr9:108319800-108321000	Active TSS	Brain Anterior Caudate	brain
23	chr9:108319800-108321000	Active TSS	Brain Cingulate Gyrus	brain
24	chr9:108319800-108321000	Active TSS	Brain Germinal Matrix	brain
25	chr9:108319800-108321000	Active TSS	Brain Hippocampus Middle	brain
26	chr9:108319800-108321000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:108319800-108321000	Active TSS	Brain Substantia Nigra	brain
28	chr9:108319800-108321000	Active TSS	Colon Smooth Muscle	Colon
29	chr9:108319800-108321000	Active TSS	Duodenum Mucosa	Duodenum
30	chr9:108319800-108321000	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr9:108319800-108321000	Active TSS	Fetal Brain Male	brain
32	chr9:108319800-108321000	Active TSS	Fetal Intestine Large	intestine
33	chr9:108319800-108321000	Active TSS	Fetal Intestine Small	intestine
34	chr9:108319800-108321000	Active TSS	Fetal Kidney	kidney
35	chr9:108319800-108321000	Active TSS	Fetal Lung	lung
36	chr9:108319800-108321000	Active TSS	Placenta	Placenta
37	chr9:108319800-108321000	Active TSS	Fetal Stomach	stomach
38	chr9:108319800-108321000	Active TSS	Fetal Thymus	thymus
39	chr9:108319800-108321000	Active TSS	Ovary	ovary
40	chr9:108319800-108321000	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr9:108319800-108321000	Active TSS	Rectal Smooth Muscle	rectum
42	chr9:108319800-108321000	Active TSS	Right Ventricle	heart
43	chr9:108319800-108321000	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr9:108319800-108321000	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr9:108319800-108321000	Active TSS	Small Intestine	intestine
46	chr9:108319800-108321000	Active TSS	Hela-S3	cervix
47	chr9:108319800-108321000	Active TSS	HSMM	muscle
48	chr9:108319800-108321000	Active TSS	K562	blood
49	chr9:108319800-108321000	Active TSS	NHEK	skin
50	chr9:108319800-108321200	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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