Variant report

Variant	rs9811753
Chromosome Location	chr3:135825793-135825794
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10935177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1153877	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs1154988	0.85[JPT][hapmap]
rs1278493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs1279831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap]
rs3957816	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs589092	0.92[CHB][hapmap];1.00[YRI][hapmap]
rs645040	0.85[JPT][hapmap]
rs661739	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs684773	0.85[JPT][hapmap]
rs687339	0.85[JPT][hapmap]
rs7372313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs895894	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9810089	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	0.85[JPT][hapmap]
rs9845457	0.82[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9811753	PCCB	cis	cerebellum	SCAN
rs9811753	PCCB	cis	parietal	SCAN
rs9811753	PPP2R3A	cis	cerebellum	SCAN
rs9811753	PCCB	cis	lymphoblastoid	seeQTL
rs9811753	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs9811753	SPSB4	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135790200-135830800	Weak transcription	Psoas Muscle	Psoas
2	chr3:135803000-135826600	Weak transcription	Liver	Liver
3	chr3:135803400-135848000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:135803600-135860600	Weak transcription	Esophagus	oesophagus
5	chr3:135803800-135832400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:135803800-135860000	Weak transcription	NHLF	lung
7	chr3:135804000-135832000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:135804000-135833200	Weak transcription	HMEC	breast
9	chr3:135805200-135832000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:135805200-135832800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:135805400-135843800	Weak transcription	NHEK	skin
12	chr3:135807400-135833200	Weak transcription	Lung	lung
13	chr3:135810000-135828800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:135810200-135827800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:135810200-135832800	Weak transcription	Brain Angular Gyrus	brain
16	chr3:135810200-135835600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:135810200-135835800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:135810400-135827000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:135810400-135828800	Weak transcription	Brain Substantia Nigra	brain
20	chr3:135810400-135830800	Weak transcription	Fetal Brain Male	brain
21	chr3:135810400-135831200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:135810400-135832000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:135810400-135832000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:135810400-135832800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:135810400-135842200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:135810400-135843000	Weak transcription	Gastric	stomach
27	chr3:135810400-135848000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:135810400-135855400	Weak transcription	Osteobl	bone
29	chr3:135810400-135859800	Weak transcription	NHDF-Ad	bronchial
30	chr3:135810400-135861000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:135818400-135832000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:135819800-135827200	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:135820200-135828200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:135820200-135834400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:135820400-135826000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:135820600-135825800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:135820800-135827000	Strong transcription	Left Ventricle	heart
38	chr3:135821200-135830600	Weak transcription	Fetal Heart	heart
39	chr3:135822000-135861000	Weak transcription	Ovary	ovary
40	chr3:135822400-135831000	Weak transcription	Fetal Kidney	kidney
41	chr3:135822400-135832800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:135822600-135831000	Weak transcription	Brain Germinal Matrix	brain
43	chr3:135822600-135832000	Weak transcription	Right Ventricle	heart
44	chr3:135822800-135830800	Weak transcription	Fetal Brain Female	brain
45	chr3:135822800-135831800	Weak transcription	Fetal Intestine Large	intestine
46	chr3:135822800-135832000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:135822800-135870000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:135823000-135826000	Weak transcription	HSMM	muscle
49	chr3:135823000-135826400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:135823000-135829200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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