Variant report

Variant	rs16871181
Chromosome Location	chr4:10641579-10641580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10027001	0.93[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10027988	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1004325	0.81[CEU][hapmap];0.93[MEX][hapmap];0.82[EUR][1000 genomes]
rs1004326	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs1019123	0.83[EUR][1000 genomes]
rs1019124	0.87[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs11942684	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12511463	0.84[EUR][1000 genomes]
rs1558199	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17383444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17467937	0.93[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1981636	0.87[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs1985450	0.81[EUR][1000 genomes]
rs2011545	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs2041212	0.84[EUR][1000 genomes]
rs2041213	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs2041214	0.85[EUR][1000 genomes]
rs2079685	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs2098057	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes]
rs2108876	0.82[EUR][1000 genomes]
rs2531179	0.81[EUR][1000 genomes]
rs2531181	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2531182	0.87[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs2531186	0.83[EUR][1000 genomes]
rs2531189	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs2531192	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2531194	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes]
rs2531195	0.86[EUR][1000 genomes]
rs2531196	0.93[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2531197	0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2531198	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2531200	0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2531201	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2531203	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2531205	0.86[CHB][hapmap];0.97[GIH][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2531207	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2531208	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes]
rs2531209	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2720352	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs2720353	0.81[EUR][1000 genomes]
rs2720354	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.84[EUR][1000 genomes]
rs2720356	0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs2720357	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2720358	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2720359	0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2720361	0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2720362	0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2720363	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2720365	0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2720368	0.87[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2720369	0.87[CEU][hapmap];0.86[CHB][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2720370	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2720371	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes]
rs2720372	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes]
rs2720374	0.80[EUR][1000 genomes]
rs2720375	0.87[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs28415493	0.85[ASN][1000 genomes]
rs28419640	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28437895	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28462041	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28475876	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28565316	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28643387	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28729939	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3948678	0.82[EUR][1000 genomes]
rs4128566	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4128567	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4128568	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4259057	0.98[ASN][1000 genomes]
rs4260534	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4320131	0.81[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs4342181	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4383612	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4399980	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4407493	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4543107	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4543108	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4583750	1.00[ASN][1000 genomes]
rs4697763	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4697764	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4697765	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4697766	0.93[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55839210	0.87[ASN][1000 genomes]
rs6448124	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6448140	0.87[ASN][1000 genomes]
rs6448160	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6811270	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6824654	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6845149	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6853762	0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs6854853	0.85[CHB][hapmap];0.80[EUR][1000 genomes]
rs7442414	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7658963	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7664095	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7671974	0.94[CEU][hapmap];0.93[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7679370	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7687180	1.00[ASN][1000 genomes]
rs9760691	0.94[ASN][1000 genomes]
rs978591	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
2	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
4	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
5	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
6	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
7	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
8	nsv1010620	chr4:9937123-10686682	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
9	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
10	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
11	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
12	nsv593727	chr4:10397327-10694991	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv517971	chr4:10399068-10893253	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv878694	chr4:10407572-10783606	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv878697	chr4:10501373-10831866	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv829860	chr4:10598743-10764854	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16871181	PSAPL1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10640600-10642600	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr4:10640600-10643200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr4:10640600-10643200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:10640600-10643400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:10640800-10643400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr4:10640800-10644000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr4:10641000-10642200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:10641000-10642400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:10641200-10641600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:10641200-10642200	Weak transcription	HMEC	breast
11	chr4:10641200-10642200	Weak transcription	NHEK	skin
12	chr4:10641200-10642400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:10641200-10642400	Weak transcription	Osteobl	bone
14	chr4:10641200-10642800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:10641200-10645400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:10641400-10641600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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