Variant report

Variant	rs2874616
Chromosome Location	chr3:157008913-157008914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:157008081..157011337-chr3:157013720..157016384,3	K562	blood:
2	chr3:157005885..157009539-chr3:157009923..157012607,4	K562	blood:
3	chr3:157007024..157009748-chr3:157011757..157013274,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10460861	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10513508	0.91[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10513509	0.82[CHB][hapmap]
rs10513510	0.86[GIH][hapmap]
rs10755111	0.91[CHB][hapmap]
rs10804778	0.82[CHB][hapmap]
rs10936063	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs10936066	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs10936074	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10936075	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10936078	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10936080	0.91[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10936081	0.91[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10936083	0.84[CHB][hapmap]
rs1157738	0.86[CEU][hapmap]
rs12488480	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap]
rs12489453	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12489799	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12490120	0.86[CHB][hapmap]
rs12492801	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs12493531	0.85[AMR][1000 genomes]
rs12494465	0.82[CHB][hapmap]
rs12495519	0.84[EUR][1000 genomes]
rs12496051	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12496111	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12629589	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12632525	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12632562	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12633429	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12634054	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12634689	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12634818	0.82[AMR][1000 genomes]
rs12635316	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12636125	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs12637476	0.82[JPT][hapmap]
rs1403104	0.87[CEU][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs1403105	0.91[CHB][hapmap]
rs1403106	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403108	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1403109	0.87[CHB][hapmap]
rs1474281	0.82[CHB][hapmap]
rs1500918	0.81[CHB][hapmap]
rs1500922	0.83[JPT][hapmap]
rs1500924	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1522392	0.91[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1546260	0.87[CHB][hapmap]
rs1568611	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16827308	0.87[CEU][hapmap]
rs16827318	0.85[ASN][1000 genomes]
rs16827322	0.87[CEU][hapmap]
rs16827352	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16827483	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1995304	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs2047648	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2173824	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2321742	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2321743	0.91[CHB][hapmap]
rs35910014	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3935750	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs4679788	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4679789	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679790	0.91[CHB][hapmap]
rs4679791	0.91[CHB][hapmap]
rs4680340	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs4680343	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs4680345	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs4680347	0.86[CEU][hapmap]
rs4680349	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680353	0.91[CHB][hapmap]
rs4680354	0.90[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5003893	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs55949516	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55953639	0.82[AMR][1000 genomes]
rs56143236	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56150358	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56313302	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59279023	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61149035	0.81[AMR][1000 genomes]
rs62276490	0.82[AMR][1000 genomes]
rs62276491	0.83[AMR][1000 genomes]
rs62276495	0.82[AMR][1000 genomes]
rs62276496	0.83[AMR][1000 genomes]
rs62276497	0.81[AMR][1000 genomes]
rs62276501	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62276502	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62276504	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62276505	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62276528	0.85[AMR][1000 genomes]
rs62278575	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62281377	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62281379	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62281383	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441115	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs6441116	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs6767619	0.82[CEU][hapmap]
rs6768074	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6780205	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6781682	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs6788214	1.00[CEU][hapmap]
rs6799567	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6805989	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs6809307	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs73154657	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73154659	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73154671	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73154682	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7610214	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7619892	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621912	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs7626589	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7631257	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7648599	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs7649737	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7652298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8925	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs924516	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs949854	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2874616	SMC4	cis	parietal	SCAN
rs2874616	CCNL1	cis	multi-tissue	Pritchard
rs2874616	PTX3	cis	cerebellum	SCAN
rs2874616	PTX3	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157000600-157015400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:157003600-157011800	Weak transcription	Fetal Lung	lung
3	chr3:157004800-157028200	Weak transcription	HUVEC	blood vessel
4	chr3:157005600-157010400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:157005600-157015000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:157006000-157011800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:157007000-157009600	Enhancers	Osteobl	bone
8	chr3:157007000-157010400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:157007200-157010200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:157007400-157009000	Enhancers	Fetal Stomach	stomach
11	chr3:157007400-157010200	Enhancers	NHLF	lung
12	chr3:157007600-157009600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:157007600-157009600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:157007600-157010200	Enhancers	HSMM	muscle
15	chr3:157007600-157012200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:157007800-157009000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:157007800-157009200	Enhancers	HSMMtube	muscle
18	chr3:157008000-157009800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:157008200-157009200	Enhancers	NH-A	brain
20	chr3:157008200-157009400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:157008400-157009800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:157008400-157010400	Enhancers	NHDF-Ad	bronchial
23	chr3:157008600-157009000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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