Variant report

Variant	rs9810089
Chromosome Location	chr3:135807609-135807610
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10935177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1153877	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs1154988	0.86[JPT][hapmap]
rs1278493	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1279831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs3957816	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs589092	0.82[CHB][hapmap]
rs645040	0.86[JPT][hapmap]
rs661739	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs684773	0.86[JPT][hapmap]
rs687339	0.86[JPT][hapmap]
rs7349597	0.80[EUR][1000 genomes]
rs7372313	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs895894	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9811753	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap]
rs9840812	0.86[JPT][hapmap]
rs9845457	0.82[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9810089	PPP2R3A	cis	cerebellum	SCAN
rs9810089	PCCB	cis	lymphoblastoid	seeQTL
rs9810089	SPSB4	cis	cerebellum	SCAN
rs9810089	PCCB	cis	parietal	SCAN
rs9810089	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs9810089	PCCB	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135771200-135809600	Weak transcription	Gastric	stomach
2	chr3:135775000-135809600	Weak transcription	Fetal Brain Male	brain
3	chr3:135775000-135809600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:135790200-135830800	Weak transcription	Psoas Muscle	Psoas
5	chr3:135790600-135809600	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:135790800-135809400	Weak transcription	Adipose Nuclei	Adipose
7	chr3:135790800-135809600	Weak transcription	Aorta	Aorta
8	chr3:135790800-135809600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:135790800-135809600	Weak transcription	Brain Anterior Caudate	brain
10	chr3:135790800-135809600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:135790800-135809600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:135794400-135809600	Weak transcription	NH-A	brain
13	chr3:135798200-135809400	Weak transcription	Brain Substantia Nigra	brain
14	chr3:135800400-135808000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:135800400-135815400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr3:135800600-135808400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:135802200-135809000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:135802600-135809800	Weak transcription	Placenta	Placenta
19	chr3:135803000-135826600	Weak transcription	Liver	Liver
20	chr3:135803200-135809000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:135803200-135809600	Weak transcription	Pancreas	Pancrea
22	chr3:135803200-135809600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:135803400-135848000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:135803600-135809400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:135803600-135809400	Weak transcription	HSMMtube	muscle
26	chr3:135803600-135809600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:135803600-135809600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:135803600-135809600	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:135803600-135809600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:135803600-135809600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:135803600-135821600	Weak transcription	Right Ventricle	heart
32	chr3:135803600-135860600	Weak transcription	Esophagus	oesophagus
33	chr3:135803800-135809200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:135803800-135809200	Weak transcription	Fetal Intestine Large	intestine
35	chr3:135803800-135809400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:135803800-135809400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:135803800-135832400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:135803800-135860000	Weak transcription	NHLF	lung
39	chr3:135804000-135809400	Weak transcription	HSMM	muscle
40	chr3:135804000-135814800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:135804000-135832000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:135804000-135833200	Weak transcription	HMEC	breast
43	chr3:135804200-135809800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:135804200-135819400	Weak transcription	Colonic Mucosa	Colon
45	chr3:135804400-135809400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:135804400-135809400	Weak transcription	Brain Germinal Matrix	brain
47	chr3:135804600-135809400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:135804600-135811400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:135804600-135822200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:135804800-135809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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