Variant report

Variant	rs2152425
Chromosome Location	chr3:160037904-160037905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10212236	0.82[ASN][1000 genomes]
rs10513551	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918749	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13403	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1451761	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1451762	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236473	0.83[JPT][hapmap]
rs1953506	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279457	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2305407	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2886825	0.81[AMR][1000 genomes]
rs3773372	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3851366	0.88[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs4091703	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41272947	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679881	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679885	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679889	0.82[ASN][1000 genomes]
rs4680576	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680579	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680580	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680585	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680587	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680588	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55687857	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55731730	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56394279	0.83[EUR][1000 genomes]
rs58322641	0.82[ASN][1000 genomes]
rs58665246	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60009222	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60460891	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62272186	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441313	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441314	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441319	0.94[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441320	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs6791261	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792612	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6793560	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6798668	0.88[CEU][hapmap]
rs6803828	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808083	0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs6809313	0.80[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs721022	0.88[ASW][hapmap];0.81[GIH][hapmap]
rs721023	0.94[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73154592	0.97[ASN][1000 genomes]
rs7356111	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611130	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7624902	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7627749	0.82[ASN][1000 genomes]
rs7627756	0.94[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7629	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7629202	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631792	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634108	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7634826	0.88[CEU][hapmap];0.88[CHB][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7645832	0.81[AMR][1000 genomes]
rs869468	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9798898	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9799314	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9968151	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2152425	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs2152425	IFT80	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
2	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
6	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:159996600-160038400	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:159997200-160046600	Weak transcription	Fetal Lung	lung
9	chr3:159999800-160047800	Weak transcription	Lung	lung
10	chr3:160010000-160047800	Weak transcription	HepG2	liver
11	chr3:160010000-160048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:160010000-160048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:160014600-160039400	Weak transcription	GM12878-XiMat	blood
14	chr3:160014800-160039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:160015000-160038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:160015000-160044000	Weak transcription	Osteobl	bone
17	chr3:160015400-160048400	Weak transcription	A549	lung
18	chr3:160015800-160048800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:160018000-160048600	Weak transcription	HSMM	muscle
20	chr3:160021200-160043400	Weak transcription	NHDF-Ad	bronchial
21	chr3:160022400-160038800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:160024400-160043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:160025400-160038800	Weak transcription	Liver	Liver
24	chr3:160025400-160056000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:160025400-160073000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:160025600-160048400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:160025600-160048600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:160025600-160072000	Weak transcription	Thymus	Thymus
29	chr3:160025600-160073200	Weak transcription	Left Ventricle	heart
30	chr3:160026200-160047600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:160029600-160050600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:160030200-160056000	Weak transcription	Fetal Stomach	stomach
33	chr3:160033200-160038400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:160033800-160049200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:160033800-160055400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:160034400-160047000	Weak transcription	Ovary	ovary
37	chr3:160034600-160038200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:160034600-160038600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:160034600-160055600	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:160034800-160039000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:160034800-160082800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:160035200-160039200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:160037000-160070200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:160037200-160055600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:160037200-160056200	Weak transcription	Primary T cells from cord blood	blood
46	chr3:160037400-160039000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:160037400-160039200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:160037400-160044800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:160037400-160048000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:160037400-160055800	Weak transcription	Primary hematopoietic stem cells	blood

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