Variant report

Variant	rs2321743
Chromosome Location	chr3:157008596-157008597
allele	C/T
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: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1014855	0.85[JPT][hapmap]
rs10513510	0.82[CHB][hapmap]
rs10513512	0.81[CHB][hapmap]
rs1074864	0.85[JPT][hapmap]
rs10755111	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804777	0.89[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10936063	0.82[CHB][hapmap]
rs10936066	0.82[CHB][hapmap]
rs10936075	0.83[ASN][1000 genomes]
rs10936077	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10936088	0.85[JPT][hapmap]
rs10936089	0.85[JPT][hapmap]
rs12486155	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12486304	0.82[AMR][1000 genomes]
rs12486955	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12490120	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12492801	0.82[CHB][hapmap]
rs12494423	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs12496111	0.81[CHB][hapmap]
rs12632562	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12633099	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12633429	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs12634905	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12636125	0.82[CHB][hapmap]
rs12637932	0.89[CEU][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1403105	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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403106	0.91[CHB][hapmap]
rs1403108	0.86[CHB][hapmap]
rs1403109	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1456104	0.85[JPT][hapmap]
rs1456109	0.85[JPT][hapmap]
rs1500923	0.83[TSI][hapmap]
rs1522393	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1546260	0.80[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1568611	0.86[CHB][hapmap]
rs1581413	0.83[TSI][hapmap]
rs1995304	0.82[CHB][hapmap]
rs2047647	0.89[CEU][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2874616	0.91[CHB][hapmap]
rs4679789	0.84[ASN][1000 genomes]
rs4679790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680340	0.82[CHB][hapmap]
rs4680343	0.82[CHB][hapmap]
rs4680345	0.81[CHB][hapmap]
rs4680352	0.91[CHB][hapmap]
rs4680353	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5003893	0.82[CHB][hapmap]
rs55734537	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6441115	0.82[CHB][hapmap]
rs6441116	0.82[CHB][hapmap]
rs6781682	0.82[CHB][hapmap]
rs6805989	0.82[CHB][hapmap]
rs6809307	0.82[CHB][hapmap]
rs73156724	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7621912	0.82[CHB][hapmap]
rs7648599	0.82[CHB][hapmap]
rs7649737	0.86[CHB][hapmap]
rs7652298	0.91[CHB][hapmap]
rs872652	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8925	0.81[CHB][hapmap]
rs9831686	0.85[JPT][hapmap]
rs9848774	0.85[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2321743	SMC4	cis	parietal	SCAN
rs2321743	SSR3	cis	cerebellum	SCAN

Chromatin state (count:22 , 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

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