Variant report

Variant	rs4561481
Chromosome Location	chr16:31259553-31259554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31204218..31206078-chr16:31258405..31260690,2	K562	blood:
2	chr16:31253838..31255685-chr16:31257972..31259890,2	K562	blood:
3	chr16:31231842..31234497-chr16:31258086..31260993,2	K562	blood:
4	chr16:31247262..31249544-chr16:31259534..31262462,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10438639	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782004	0.81[JPT][hapmap]
rs11150613	0.85[CHB][hapmap]
rs11574631	0.84[CHB][hapmap]
rs11641624	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11645526	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11864632	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs11865830	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12449089	0.81[ASN][1000 genomes]
rs12929077	0.95[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13336592	0.95[CEU][hapmap]
rs17708638	0.86[CEU][hapmap]
rs1808430	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2011491	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2359661	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs2735393	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs3087796	0.82[CHB][hapmap]
rs3764327	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815801	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077810	0.84[CHB][hapmap]
rs4447446	0.84[ASN][1000 genomes]
rs4459557	0.85[CHB][hapmap]
rs4597342	0.84[CHB][hapmap]
rs4889537	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs4889538	0.80[EUR][1000 genomes]
rs4889633	0.80[EUR][1000 genomes]
rs4889639	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4889640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889644	0.81[EUR][1000 genomes]
rs60660286	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6565225	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7186832	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7187143	0.95[CEU][hapmap];0.84[JPT][hapmap]
rs7193943	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7196256	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7206295	0.84[CHB][hapmap]
rs741810	0.95[CEU][hapmap]
rs7499192	0.92[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8044075	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8047985	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8048583	0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8051304	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056505	0.95[CEU][hapmap]
rs8057320	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8060268	0.84[CHB][hapmap]
rs8062426	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889549	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889551	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929868	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9673519	0.87[CHB][hapmap]
rs9923270	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9938177	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
2	nsv1066073	chr16:31219071-31278572	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4561481	PYDC1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31250400-31262600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:31256600-31264000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr16:31256600-31264200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr16:31257800-31260200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr16:31258000-31263400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr16:31259000-31260600	Enhancers	HMEC	breast
7	chr16:31259000-31260800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:31259200-31259600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr16:31259200-31260400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr16:31259200-31260400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr16:31259200-31260400	Enhancers	NHEK	skin
12	chr16:31259200-31260600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr16:31259200-31260600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr16:31259200-31261600	Enhancers	K562	blood
15	chr16:31259400-31259800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr16:31259400-31260400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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