Variant report

Variant	rs3815801
Chromosome Location	chr16:31276937-31276938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31270699..31273371-chr16:31276561..31278848,2	K562	blood:
2	chr16:31275132..31278473-chr16:31280951..31284251,6	MCF-7	breast:
3	chr16:31270699..31272773-chr16:31275634..31278061,2	K562	blood:
4	chr16:31275104..31276971-chr16:31278723..31280338,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252876	Chromatin interaction
ENSG00000169896	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10438639	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1106398	0.81[CHB][hapmap]
rs11150610	0.84[JPT][hapmap]
rs11150613	0.86[CHB][hapmap]
rs1143682	0.84[JPT][hapmap]
rs11574630	0.81[CHB][hapmap]
rs11574631	0.86[CHB][hapmap]
rs11641624	0.91[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11645526	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11863627	0.81[EUR][1000 genomes]
rs11864632	0.84[CEU][hapmap]
rs11865830	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12449089	0.83[ASN][1000 genomes]
rs12929077	0.83[CEU][hapmap];0.88[JPT][hapmap]
rs13336592	0.80[CEU][hapmap]
rs1808430	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2011491	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2359661	0.81[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2735393	0.83[CEU][hapmap]
rs3087796	0.84[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs3764327	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4077810	0.86[CHB][hapmap]
rs4447446	0.87[ASN][1000 genomes]
rs4459557	0.86[CHB][hapmap]
rs4561481	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4597342	0.86[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs4889537	0.83[CEU][hapmap]
rs4889639	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4889640	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889644	0.87[EUR][1000 genomes]
rs60660286	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6565225	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7186832	0.83[CEU][hapmap]
rs7187143	0.84[CEU][hapmap]
rs7193943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7196256	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7206295	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs741810	0.83[CEU][hapmap]
rs7499192	0.83[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8044075	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8047985	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8048583	0.96[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8051304	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8056505	0.83[CEU][hapmap]
rs8057320	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8060268	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs8062426	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs889549	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs889551	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs929868	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9673519	0.89[CHB][hapmap]
rs9923270	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9938177	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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
rs3815801	PYDC1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31269800-31277800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr16:31272000-31277000	Enhancers	Primary B cells from peripheral blood	blood
3	chr16:31272200-31277000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:31272200-31277600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr16:31272400-31277400	Enhancers	Primary hematopoietic stem cells	blood
6	chr16:31273000-31277000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr16:31274000-31277600	Enhancers	Primary B cells from cord blood	blood
8	chr16:31274200-31277600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
9	chr16:31275800-31277600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr16:31276000-31277600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr16:31276000-31277800	Enhancers	Fetal Thymus	thymus
12	chr16:31276200-31277400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr16:31276200-31277400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr16:31276200-31277400	Enhancers	Colonic Mucosa	Colon
15	chr16:31276200-31277600	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr16:31276200-31277600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr16:31276400-31277000	Enhancers	HSMMtube	muscle
18	chr16:31276400-31277200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:31276400-31277200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
20	chr16:31276400-31277200	Flanking Active TSS	A549	lung
21	chr16:31276400-31277400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr16:31276400-31277400	Enhancers	HMEC	breast
23	chr16:31276400-31277600	Flanking Active TSS	GM12878-XiMat	blood
24	chr16:31276400-31277800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr16:31276400-31277800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr16:31276400-31278000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr16:31276600-31277200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr16:31276600-31277200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr16:31276600-31277400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr16:31276600-31277400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr16:31276600-31277600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr16:31276600-31277600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr16:31276600-31277600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr16:31276600-31277600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr16:31276600-31277600	Genic enhancers	Spleen	Spleen
36	chr16:31276600-31277600	Genic enhancers	Monocytes-CD14+_RO01746	blood
37	chr16:31276600-31277800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr16:31276600-31279600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr16:31276800-31277000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr16:31276800-31277000	Enhancers	Duodenum Mucosa	Duodenum
41	chr16:31276800-31277000	Enhancers	Placenta	Placenta
42	chr16:31276800-31277200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr16:31276800-31277200	Enhancers	Lung	lung
44	chr16:31276800-31277200	Flanking Active TSS	NHEK	skin
45	chr16:31276800-31277400	Enhancers	Pancreas	Pancrea
46	chr16:31276800-31277600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr16:31276800-31277600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links