Variant report

Variant	rs171519
Chromosome Location	chr3:136713355-136713356
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs108858	0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11711599	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054220	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629000	1.00[CHB][hapmap]
rs13095028	0.90[CHD][hapmap];0.84[JPT][hapmap]
rs13095034	0.87[ASN][1000 genomes]
rs1385306	0.82[ASN][1000 genomes]
rs1406539	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1620455	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1654900	0.82[ASN][1000 genomes]
rs1654901	0.82[ASN][1000 genomes]
rs1654924	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1682339	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1682361	0.82[ASN][1000 genomes]
rs1682362	0.82[ASN][1000 genomes]
rs1682363	0.82[ASN][1000 genomes]
rs1682364	0.82[ASN][1000 genomes]
rs1682365	0.82[ASN][1000 genomes]
rs1682366	0.82[ASN][1000 genomes]
rs16844241	1.00[CHB][hapmap]
rs181732	0.82[ASN][1000 genomes]
rs183120	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183121	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2117008	0.83[ASN][1000 genomes]
rs2344092	0.84[ASN][1000 genomes]
rs361227	0.82[ASN][1000 genomes]
rs361228	0.82[ASN][1000 genomes]
rs361229	0.82[ASN][1000 genomes]
rs361232	0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs361233	0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs361234	0.85[ASN][1000 genomes]
rs361235	0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs361237	0.81[MKK][hapmap]
rs361238	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361240	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361249	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361253	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678275	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4678447	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs55781515	0.82[ASN][1000 genomes]
rs71620537	0.87[ASN][1000 genomes]
rs7610507	1.00[CHB][hapmap]
rs7631541	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7648198	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs835627	0.82[ASN][1000 genomes]
rs835629	0.82[ASN][1000 genomes]
rs835630	0.82[ASN][1000 genomes]
rs835631	0.82[ASN][1000 genomes]
rs835636	1.00[CHD][hapmap]
rs835637	1.00[CHD][hapmap]
rs835638	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs835652	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs9681468	0.81[ASN][1000 genomes]
rs9682783	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9845076	0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs9845460	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9850024	0.82[ASN][1000 genomes]
rs9854795	0.82[ASN][1000 genomes]
rs9874615	0.82[ASN][1000 genomes]
rs9875855	0.87[ASN][1000 genomes]
rs999038	0.82[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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs171519	PCCB	cis	parietal	SCAN
rs171519	PCCB	cis	cerebellum	SCAN
rs171519	SPSB4	cis	cerebellum	SCAN
rs171519	PPP2R3A	cis	parietal	SCAN
rs171519	IL20RB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136703800-136713600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:136703800-136732400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:136704000-136713400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:136704000-136713400	Weak transcription	Pancreas	Pancrea
5	chr3:136704000-136714600	Weak transcription	Right Ventricle	heart
6	chr3:136704000-136730600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:136704400-136713400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:136704600-136713600	Weak transcription	HSMM	muscle
9	chr3:136704800-136731000	Weak transcription	HSMMtube	muscle
10	chr3:136706800-136715800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:136707600-136713400	Weak transcription	Fetal Stomach	stomach
12	chr3:136708200-136714400	Enhancers	HMEC	breast
13	chr3:136708800-136715600	Enhancers	Fetal Thymus	thymus
14	chr3:136708800-136720000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:136709000-136713400	Weak transcription	Colonic Mucosa	Colon
16	chr3:136709000-136713400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:136709400-136713400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:136709600-136713400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:136709800-136713400	Weak transcription	Lung	lung
20	chr3:136710000-136713400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:136710000-136731000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:136711800-136713400	Weak transcription	Esophagus	oesophagus
23	chr3:136712200-136713400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:136712200-136713600	Weak transcription	Thymus	Thymus
25	chr3:136712200-136714200	Enhancers	NHEK	skin
26	chr3:136712200-136714600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:136712800-136713400	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr3:136712800-136715000	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:136713000-136715200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:136713000-136715800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:136713200-136713400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:136713200-136713400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:136713200-136713400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:136713200-136713400	Enhancers	Brain Substantia Nigra	brain
35	chr3:136713200-136713400	Enhancers	Osteobl	bone
36	chr3:136713200-136714000	Enhancers	Hela-S3	cervix
37	chr3:136713200-136714400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr3:136713200-136714400	Enhancers	Fetal Brain Female	brain
39	chr3:136713200-136714600	Enhancers	Small Intestine	intestine
40	chr3:136713200-136714800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:136713200-136714800	Enhancers	HUVEC	blood vessel
42	chr3:136713200-136715000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:136713200-136715000	Enhancers	Brain Anterior Caudate	brain
44	chr3:136713200-136715000	Enhancers	Brain Germinal Matrix	brain
45	chr3:136713200-136715000	Enhancers	Ovary	ovary
46	chr3:136713200-136715000	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr3:136713200-136715200	Enhancers	Adipose Nuclei	Adipose
48	chr3:136713200-136715200	Enhancers	Brain Angular Gyrus	brain
49	chr3:136713200-136715200	Enhancers	Right Atrium	heart
50	chr3:136713200-136715600	Enhancers	Cortex derived primary cultured neurospheres	brain

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