Variant report

Variant	rs875812
Chromosome Location	chr7:48462563-48462564
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10228865	0.81[AMR][1000 genomes]
rs10230009	0.82[AMR][1000 genomes]
rs10234238	0.91[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs10234633	0.81[AMR][1000 genomes]
rs10238444	0.82[AMR][1000 genomes]
rs10239702	0.82[AMR][1000 genomes]
rs10242000	0.82[AMR][1000 genomes]
rs10246994	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs10260525	0.82[AMR][1000 genomes]
rs10260644	0.82[AMR][1000 genomes]
rs10262407	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10262568	0.82[AMR][1000 genomes]
rs10270214	0.82[AMR][1000 genomes]
rs10272707	0.82[AMR][1000 genomes]
rs10273249	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10273640	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10274174	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10275998	0.81[AMR][1000 genomes]
rs10480938	0.82[AMR][1000 genomes]
rs10480939	0.82[AMR][1000 genomes]
rs10480940	0.82[AMR][1000 genomes]
rs10499681	0.91[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs12666688	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs12667933	0.95[CEU][hapmap];0.82[AMR][1000 genomes]
rs12668898	0.82[AMR][1000 genomes]
rs12669314	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs12669327	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs12718266	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12718271	0.82[AMR][1000 genomes]
rs12718274	0.91[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs13221884	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs13227183	0.91[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs13233421	0.91[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs13236501	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13238013	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs13243091	0.90[CEU][hapmap];0.85[AMR][1000 genomes]
rs13245697	0.83[AMR][1000 genomes]
rs13247279	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13307295	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1433497	0.82[AMR][1000 genomes]
rs1433498	0.91[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs1433504	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs1433507	0.95[CEU][hapmap];0.82[AMR][1000 genomes]
rs1433508	0.83[AMR][1000 genomes]
rs1433509	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1433510	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1594761	0.82[AMR][1000 genomes]
rs1594762	0.82[AMR][1000 genomes]
rs17662275	0.82[AMR][1000 genomes]
rs17729791	0.82[AMR][1000 genomes]
rs17729821	0.82[AMR][1000 genomes]
rs17729827	0.82[AMR][1000 genomes]
rs17729863	0.82[AMR][1000 genomes]
rs17729875	0.82[AMR][1000 genomes]
rs2217709	0.82[AMR][1000 genomes]
rs2362304	0.82[AMR][1000 genomes]
rs28369084	0.85[AMR][1000 genomes]
rs28408591	0.82[AMR][1000 genomes]
rs28454544	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28589871	0.82[AMR][1000 genomes]
rs28617685	0.82[AMR][1000 genomes]
rs28687524	0.82[AMR][1000 genomes]
rs28707009	0.82[AMR][1000 genomes]
rs28796433	0.82[AMR][1000 genomes]
rs34222830	0.82[AMR][1000 genomes]
rs34541457	0.85[AMR][1000 genomes]
rs34563223	0.85[AMR][1000 genomes]
rs34691991	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34832520	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34891690	0.82[AMR][1000 genomes]
rs35051826	0.82[AMR][1000 genomes]
rs35132202	0.82[AMR][1000 genomes]
rs35146218	0.82[AMR][1000 genomes]
rs35375355	0.82[AMR][1000 genomes]
rs35598378	0.82[AMR][1000 genomes]
rs35754209	0.85[AMR][1000 genomes]
rs35972471	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36035836	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36119580	0.83[AMR][1000 genomes]
rs5028265	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5028266	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5028267	0.90[CEU][hapmap]
rs55734752	0.82[AMR][1000 genomes]
rs56244801	0.82[AMR][1000 genomes]
rs56945649	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60560717	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66976409	0.82[AMR][1000 genomes]
rs67591654	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6942708	0.85[AMR][1000 genomes]
rs6946085	0.81[AMR][1000 genomes]
rs6957156	0.91[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs6978616	0.82[AMR][1000 genomes]
rs7357239	0.83[AMR][1000 genomes]
rs7783082	0.82[AMR][1000 genomes]
rs7790171	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs7794355	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs7795217	0.82[AMR][1000 genomes]
rs7809680	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs875810	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs875811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9632787	0.85[AMR][1000 genomes]
rs9632788	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv533811	chr7:48313757-48482470	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs875812	PKD1L1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48449400-48467800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:48460000-48465800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:48461200-48462800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr7:48461600-48464600	Weak transcription	HMEC	breast
5	chr7:48461600-48464600	Weak transcription	NHEK	skin
6	chr7:48461600-48466200	Weak transcription	Osteobl	bone
7	chr7:48461600-48466600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:48461800-48466000	Weak transcription	NH-A	brain
9	chr7:48462000-48464600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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