Variant report

Variant	rs4680349
Chromosome Location	chr3:156973544-156973545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 157 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs10460861	0.81[AMR][1000 genomes]
rs10513508	0.91[CEU][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs10513510	0.81[GIH][hapmap]
rs10755111	0.82[CHB][hapmap]
rs10936061	0.84[EUR][1000 genomes]
rs10936062	0.84[EUR][1000 genomes]
rs10936063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs10936064	0.83[EUR][1000 genomes]
rs10936065	0.83[EUR][1000 genomes]
rs10936066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs10936067	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10936068	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10936069	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10936074	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10936075	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10936078	0.89[CEU][hapmap];0.86[AMR][1000 genomes]
rs10936080	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs10936081	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs1157738	0.86[CEU][hapmap]
rs12488480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs12489453	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489799	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490836	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12492801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12493531	0.87[AMR][1000 genomes]
rs12496051	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12497891	0.85[EUR][1000 genomes]
rs12629589	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12630209	0.83[EUR][1000 genomes]
rs12632525	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12632562	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12633429	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12634818	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12635088	0.84[EUR][1000 genomes]
rs12635316	0.86[AMR][1000 genomes]
rs12636125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1403104	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs1403105	0.82[CHB][hapmap]
rs1403106	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1403108	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs1500922	0.87[YRI][hapmap]
rs1500924	0.91[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes]
rs1522392	0.91[CEU][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes]
rs1568611	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16827308	0.87[CEU][hapmap]
rs16827318	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16827322	0.87[CEU][hapmap];0.87[MKK][hapmap]
rs16827352	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16827483	0.86[AMR][1000 genomes]
rs17552941	0.84[EUR][1000 genomes]
rs1995304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2047648	0.86[CEU][hapmap];0.86[AMR][1000 genomes]
rs2321742	0.92[AMR][1000 genomes]
rs2321743	0.82[CHB][hapmap]
rs2874616	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35910014	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3935750	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs41272613	0.84[EUR][1000 genomes]
rs4371471	0.82[EUR][1000 genomes]
rs4383467	0.83[EUR][1000 genomes]
rs4413278	0.85[EUR][1000 genomes]
rs4608646	0.83[EUR][1000 genomes]
rs4679788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679789	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4679790	0.82[CHB][hapmap]
rs4679791	0.82[CHB][hapmap]
rs4680340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs4680343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4680345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs4680347	0.86[CEU][hapmap]
rs4680352	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680353	0.82[CHB][hapmap]
rs4680354	0.90[CEU][hapmap];0.86[AMR][1000 genomes]
rs5003893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs55828309	0.85[EUR][1000 genomes]
rs55835412	0.84[EUR][1000 genomes]
rs55949516	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55953639	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56078410	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56143236	0.94[AMR][1000 genomes]
rs56150358	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56263456	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56313302	0.86[AMR][1000 genomes]
rs57322659	0.84[EUR][1000 genomes]
rs57511361	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59210914	0.81[EUR][1000 genomes]
rs59279023	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59485606	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60153077	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61149035	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62274129	0.81[EUR][1000 genomes]
rs62274155	0.83[EUR][1000 genomes]
rs62274156	0.83[EUR][1000 genomes]
rs62274159	0.85[EUR][1000 genomes]
rs62276460	0.85[EUR][1000 genomes]
rs62276461	0.85[EUR][1000 genomes]
rs62276462	0.85[EUR][1000 genomes]
rs62276465	0.83[EUR][1000 genomes]
rs62276470	0.84[EUR][1000 genomes]
rs62276471	0.84[EUR][1000 genomes]
rs62276474	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62276475	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62276479	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62276480	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62276489	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62276490	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62276491	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62276495	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62276496	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62276497	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62276501	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276502	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276504	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276505	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276528	0.87[AMR][1000 genomes]
rs62278575	0.86[AMR][1000 genomes]
rs62281377	0.86[AMR][1000 genomes]
rs62281379	0.86[AMR][1000 genomes]
rs62281383	0.86[AMR][1000 genomes]
rs6441115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6441116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6441119	0.85[EUR][1000 genomes]
rs6767619	0.82[CEU][hapmap]
rs6768052	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6780205	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781682	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs6788214	1.00[CEU][hapmap]
rs6792479	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6799567	0.91[CEU][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes]
rs6805989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6806232	0.85[EUR][1000 genomes]
rs6809307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs73154633	0.82[EUR][1000 genomes]
rs73154649	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73154657	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73154659	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73154671	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73154682	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73873800	0.83[EUR][1000 genomes]
rs7610214	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7619892	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7626589	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631257	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs7633004	0.84[EUR][1000 genomes]
rs7648599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7649737	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[AMR][1000 genomes]
rs7652298	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8180056	0.84[EUR][1000 genomes]
rs8180057	0.84[EUR][1000 genomes]
rs8925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs924516	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs949854	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4680349	PTX3	cis	cerebellum	SCAN
rs4680349	PTX3	cis	parietal	SCAN
rs4680349	SMC4	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156967000-156979000	Weak transcription	HSMMtube	muscle
2	chr3:156967200-156974600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:156967200-156974600	Weak transcription	Osteobl	bone
4	chr3:156967200-156975000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:156967200-156982000	Weak transcription	Lung	lung
6	chr3:156967200-156989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:156967200-157000000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:156967200-157000000	Weak transcription	NH-A	brain
9	chr3:156967200-157007800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:156968000-156976400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:156968000-156981800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:156968200-156973600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:156968600-156973600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:156970400-156973800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:156970800-156974400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:156972800-156978400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:156973000-156974200	Strong transcription	HUVEC	blood vessel
18	chr3:156973200-156974200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:156973400-156973600	Weak transcription	Aorta	Aorta
20	chr3:156973400-156973800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:156973400-156974000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:156973400-156974200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:156973400-156974400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:156973400-156974600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr3:156973400-156975200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:156973400-156975400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr3:156973400-156975400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:156973400-156975600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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