Variant report

Variant	rs9877176
Chromosome Location	chr3:140160906-140160907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140160036..140161866-chr3:140164735..140166930,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10935381	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935382	0.84[JPT][hapmap]
rs10935383	0.83[CHB][hapmap];0.85[AMR][1000 genomes]
rs11923323	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11925150	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11926917	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11926945	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12486034	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13085384	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13092991	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1427778	0.83[CHB][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs1427781	0.83[CHB][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes]
rs1427784	0.83[CHB][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes]
rs16850245	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2114859	0.83[CHB][hapmap]
rs347332	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs347335	0.85[CHD][hapmap]
rs34769437	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35757937	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846016	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3909790	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3909791	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3912204	0.86[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4142787	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4611778	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62266407	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66934556	0.85[AMR][1000 genomes]
rs6771366	0.83[CHB][hapmap];0.80[MEX][hapmap]
rs7614605	0.84[JPT][hapmap]
rs9757210	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9882815	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv460867	chr3:140007294-140180563	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv591861	chr3:140007294-140180563	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv818169	chr3:140014763-140182046	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1001430	chr3:140016999-140186498	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv998953	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv536731	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv829741	chr3:140021063-140183294	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1004500	chr3:140021594-140189148	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv460868	chr3:140124599-140169657	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv591862	chr3:140124599-140169657	Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv591863	chr3:140126067-140274442	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9877176	PLS1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140153600-140178400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:140158200-140189000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:140158600-140161800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:140159400-140162000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:140159800-140161200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:140160200-140161400	Weak transcription	Osteobl	bone
7	chr3:140160400-140161400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:140160400-140161600	Weak transcription	HSMMtube	muscle
9	chr3:140160600-140161000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:140160600-140162800	Enhancers	Left Ventricle	heart
11	chr3:140160800-140161200	Weak transcription	NHDF-Ad	bronchial
12	chr3:140160800-140161400	Weak transcription	HSMM	muscle
13	chr3:140160800-140162400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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