Variant report

Variant	rs10935177
Chromosome Location	chr3:135851077-135851078
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1153877	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs1154988	1.00[JPT][hapmap]
rs1278493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1279086	0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs1279425	0.86[JPT][hapmap]
rs1279831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs1279840	0.86[JPT][hapmap]
rs1711171	0.86[JPT][hapmap]
rs3755636	0.86[JPT][hapmap]
rs3957816	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4678428	0.86[JPT][hapmap]
rs483465	0.86[JPT][hapmap]
rs518972	0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs548288	0.86[JPT][hapmap]
rs553018	0.92[CHB][hapmap]
rs556788	0.85[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs576771	0.81[JPT][hapmap]
rs589092	0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs606725	0.86[JPT][hapmap]
rs642075	0.84[EUR][1000 genomes]
rs645040	1.00[JPT][hapmap]
rs650326	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs661739	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs684773	1.00[JPT][hapmap]
rs687339	1.00[JPT][hapmap]
rs696081	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs7349597	0.84[EUR][1000 genomes]
rs7372313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs895894	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9810089	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]
rs9811753	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]
rs9840812	1.00[JPT][hapmap]
rs9845457	0.82[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10935177	PCCB	cis	cerebellum	SCAN
rs10935177	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs10935177	PCCB	cis	parietal	SCAN
rs10935177	PCCB	cis	lymphoblastoid	seeQTL
rs10935177	PCCB	cis	multi-tissue	Pritchard
rs10935177	PPP2R3A	cis	cerebellum	SCAN
rs10935177	SPSB4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135803600-135860600	Weak transcription	Esophagus	oesophagus
2	chr3:135803800-135860000	Weak transcription	NHLF	lung
3	chr3:135810400-135855400	Weak transcription	Osteobl	bone
4	chr3:135810400-135859800	Weak transcription	NHDF-Ad	bronchial
5	chr3:135810400-135861000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:135822000-135861000	Weak transcription	Ovary	ovary
7	chr3:135822800-135870000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:135823200-135868400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:135824400-135854400	Weak transcription	Pancreas	Pancrea
10	chr3:135831400-135869400	Weak transcription	Psoas Muscle	Psoas
11	chr3:135831400-135874800	Weak transcription	Fetal Brain Male	brain
12	chr3:135831800-135859800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:135833000-135853200	Weak transcription	Fetal Heart	heart
14	chr3:135833000-135859800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:135833000-135860600	Weak transcription	Right Ventricle	heart
16	chr3:135833200-135860600	Weak transcription	HSMMtube	muscle
17	chr3:135843400-135866400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:135843800-135873800	Weak transcription	Colonic Mucosa	Colon
19	chr3:135844400-135859800	Weak transcription	HSMM	muscle
20	chr3:135845200-135854000	Weak transcription	Gastric	stomach
21	chr3:135845600-135855400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:135845600-135855600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:135845600-135859800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:135845600-135860200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:135845600-135860200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:135845600-135860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:135845600-135860600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:135845600-135863000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:135845600-135864000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:135845600-135869600	Weak transcription	Fetal Lung	lung
31	chr3:135845600-135880400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:135845800-135853800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:135845800-135853800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:135845800-135853800	Weak transcription	Left Ventricle	heart
35	chr3:135845800-135855400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:135845800-135860600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:135845800-135860600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:135845800-135860600	Weak transcription	Aorta	Aorta
39	chr3:135845800-135861800	Weak transcription	Fetal Stomach	stomach
40	chr3:135845800-135864000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:135845800-135866000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:135846200-135851400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:135846200-135859600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:135846200-135859600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:135846200-135859800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:135846200-135863600	Weak transcription	Brain Germinal Matrix	brain
47	chr3:135846200-135864200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:135846400-135860000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:135846600-135860800	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:135850800-135866000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links