Variant report

Variant	rs4083233
Chromosome Location	chr7:48499310-48499311
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10227179	0.94[AFR][1000 genomes]
rs10227187	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs10230786	0.82[YRI][hapmap]
rs10233704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10237159	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10240667	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10251517	0.84[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs10251627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1025520	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10256255	0.92[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10267753	0.92[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10268515	0.94[AFR][1000 genomes]
rs10276989	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs10280481	0.92[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1030707	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11766842	0.84[AFR][1000 genomes]
rs12533158	0.84[AFR][1000 genomes]
rs12533748	0.84[AFR][1000 genomes]
rs1433499	0.92[AFR][1000 genomes]
rs1433500	0.92[AFR][1000 genomes]
rs17132342	0.94[AFR][1000 genomes]
rs17132359	0.85[AFR][1000 genomes]
rs1836092	0.92[AFR][1000 genomes]
rs1881079	0.88[AFR][1000 genomes]
rs1881080	0.88[AFR][1000 genomes]
rs1975194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2043391	0.86[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2043392	0.92[AFR][1000 genomes]
rs2043393	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2043394	0.94[AFR][1000 genomes]
rs2362310	0.86[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28627154	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2885482	0.88[AFR][1000 genomes]
rs35345934	0.92[AFR][1000 genomes]
rs4256548	0.88[AFR][1000 genomes]
rs4472462	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4621756	0.90[AFR][1000 genomes]
rs4623358	0.83[AFR][1000 genomes]
rs4642585	0.87[AFR][1000 genomes]
rs4917019	0.90[AFR][1000 genomes]
rs4917020	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4917140	0.83[AFR][1000 genomes]
rs4917141	0.92[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4917142	0.92[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4917143	0.92[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4917144	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4917145	0.92[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4917146	0.92[AFR][1000 genomes]
rs4917147	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4917149	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4917150	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4917152	0.84[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4917153	0.84[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4917154	0.84[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4917155	0.84[AFR][1000 genomes]
rs735069	0.88[AFR][1000 genomes]
rs735070	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7782619	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7789206	0.84[AFR][1000 genomes]
rs7810026	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817336	chr7:48238233-48563988	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1022980	chr7:48243227-48567060	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv538833	chr7:48243227-48567060	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1022578	chr7:48244414-48584664	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1023575	chr7:48244414-48586685	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1015183	chr7:48244414-48588598	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1032221	chr7:48302789-48546684	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1015399	chr7:48321542-48544359	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2761325	chr7:48409639-48557382	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv888007	chr7:48467581-48533508	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv830992	chr7:48497408-48686442	Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4083233	PKD1L1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48468000-48500000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:48495200-48503200	Weak transcription	Spleen	Spleen
3	chr7:48498400-48499400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr7:48498400-48499400	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr7:48498800-48499600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:48498800-48500200	Enhancers	HMEC	breast
7	chr7:48499200-48499400	Genic enhancers	Primary neutrophils fromperipheralblood	blood

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