Variant report

Variant	rs3020016
Chromosome Location	chr11:93915248-93915249
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93861104..93863451-chr11:93914725..93916276,2	K562	blood:
2	chr11:93914625..93916953-chr11:94227203..94228744,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110218	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1014499	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10458852	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10765657	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10765658	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10765660	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10831169	0.93[EUR][1000 genomes]
rs10831173	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10831174	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10831176	0.89[EUR][1000 genomes]
rs10831184	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11020678	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11020679	0.89[EUR][1000 genomes]
rs11020703	0.86[EUR][1000 genomes]
rs11020719	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12366039	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12792677	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12808853	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1361929	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1541301	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16920039	0.92[CEU][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs1789652	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1792632	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1857680	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1944436	0.89[EUR][1000 genomes]
rs2000956	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2156627	0.89[EUR][1000 genomes]
rs3020004	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4597032	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4753131	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4753132	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4753569	0.83[AMR][1000 genomes]
rs480710	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs581771	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs613234	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs655358	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689315	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7118270	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7927338	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7927496	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7936241	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7944234	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898184	chr11:93741612-93969726	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1046092	chr11:93833446-93964452	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv898185	chr11:93851048-93927529	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv469980	chr11:93864321-93962121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv468795	chr11:93864321-93964917	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv555966	chr11:93864321-93964917	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3020016	RP11-680H20.2	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93885200-93916200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:93897800-93920000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:93900400-93916000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:93901200-93917200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:93901400-93921200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:93904800-93920000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:93905400-93919600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:93907200-93919600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:93909200-93917400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:93909400-93917400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:93909400-93918400	Weak transcription	Fetal Heart	heart
12	chr11:93909600-93917000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:93909800-93917200	Weak transcription	HUVEC	blood vessel
14	chr11:93910000-93916800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:93910400-93919000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr11:93910600-93915600	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr11:93910600-93916200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:93910600-93917200	Strong transcription	Dnd41	blood
19	chr11:93910600-93919200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:93910800-93915400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:93910800-93915400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr11:93910800-93915600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:93910800-93915600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:93910800-93915800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:93910800-93916000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr11:93910800-93916000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:93910800-93916000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr11:93910800-93916800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:93910800-93917000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:93910800-93917000	Strong transcription	Left Ventricle	heart
31	chr11:93911000-93915400	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr11:93911000-93915400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:93911000-93916000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr11:93911200-93915600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:93911200-93916200	Strong transcription	Primary T cells from cord blood	blood
36	chr11:93911200-93916800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:93911200-93917000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr11:93911400-93915600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:93911400-93915600	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr11:93911400-93916000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:93911400-93916000	Strong transcription	Adipose Nuclei	Adipose
42	chr11:93911400-93916800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr11:93911600-93915400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:93911600-93915400	Strong transcription	Fetal Brain Female	brain
45	chr11:93911600-93916800	Strong transcription	Fetal Thymus	thymus
46	chr11:93911600-93917000	Weak transcription	A549	lung
47	chr11:93911600-93917200	Weak transcription	Colonic Mucosa	Colon
48	chr11:93911800-93916200	Strong transcription	GM12878-XiMat	blood
49	chr11:93912200-93916200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr11:93912200-93921000	Weak transcription	Brain Anterior Caudate	brain

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