Variant report

Variant	rs33988592
Chromosome Location	chr3:121415610-121415611
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	chr3:121410605..121412788-chr3:121413603..121415735,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11707504	0.82[EUR][1000 genomes]
rs11707518	0.82[EUR][1000 genomes]
rs11707716	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714406	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11715951	0.81[EUR][1000 genomes]
rs11716984	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719093	0.82[EUR][1000 genomes]
rs11719458	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11720859	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11721318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061326	0.82[EUR][1000 genomes]
rs13062684	0.82[EUR][1000 genomes]
rs13072618	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072767	0.82[EUR][1000 genomes]
rs13074834	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077135	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083794	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13087578	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090660	0.87[EUR][1000 genomes]
rs13090798	0.82[EUR][1000 genomes]
rs13433692	0.82[EUR][1000 genomes]
rs13434284	0.82[EUR][1000 genomes]
rs1573819	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17691170	0.89[EUR][1000 genomes]
rs2070180	0.88[EUR][1000 genomes]
rs28660600	0.82[EUR][1000 genomes]
rs28674947	0.81[EUR][1000 genomes]
rs34086988	0.88[EUR][1000 genomes]
rs34667636	0.88[EUR][1000 genomes]
rs35679661	0.82[EUR][1000 genomes]
rs35988617	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36142735	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732408	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772128	0.86[EUR][1000 genomes]
rs3772130	0.86[EUR][1000 genomes]
rs4280673	0.81[EUR][1000 genomes]
rs4298081	0.81[EUR][1000 genomes]
rs4311252	0.81[EUR][1000 genomes]
rs4413346	0.82[EUR][1000 genomes]
rs55643643	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55657471	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56314138	0.88[EUR][1000 genomes]
rs62268732	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62268734	0.92[ASN][1000 genomes]
rs66653099	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768621	0.81[EUR][1000 genomes]
rs6791046	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427165	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289177	0.80[EUR][1000 genomes]
rs9812228	0.82[EUR][1000 genomes]
rs9816844	0.81[EUR][1000 genomes]
rs9839617	0.81[EUR][1000 genomes]
rs9841595	0.82[EUR][1000 genomes]
rs9878086	0.82[EUR][1000 genomes]
rs9883467	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv980114	chr3:121413547-121415961	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs33988592	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs33988592	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs33988592	IQCB1	cis	Whole Blood	GTEx
rs33988592	HCLS1	cis	Whole Blood	GTEx
rs33988592	IQCB1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:121396800-121435600	Weak transcription	Psoas Muscle	Psoas
3	chr3:121399000-121425400	Weak transcription	Pancreas	Pancrea
4	chr3:121399000-121426400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:121399000-121440400	Weak transcription	K562	blood
6	chr3:121399200-121416800	Weak transcription	Fetal Stomach	stomach
7	chr3:121401200-121416800	Weak transcription	Spleen	Spleen
8	chr3:121401200-121429400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:121401200-121434000	Weak transcription	Gastric	stomach
10	chr3:121404000-121432800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:121407400-121429400	Weak transcription	Esophagus	oesophagus
12	chr3:121408200-121417400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:121408200-121422400	Strong transcription	Placenta	Placenta
14	chr3:121408200-121428400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:121408400-121421000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:121408400-121421600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:121408600-121417600	Strong transcription	Fetal Brain Female	brain
18	chr3:121408600-121417600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr3:121408600-121417800	Strong transcription	HSMMtube	muscle
20	chr3:121408600-121418200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:121408600-121420400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:121408600-121421400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr3:121408600-121421600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:121408600-121421600	Strong transcription	Primary T cells from cord blood	blood
25	chr3:121408600-121421800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:121408600-121421800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:121408600-121422800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:121408600-121424600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:121408600-121424800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:121408600-121424800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr3:121408600-121427400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:121408600-121428200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:121408800-121415800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:121408800-121422800	Strong transcription	Primary B cells from cord blood	blood
35	chr3:121408800-121424800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:121409000-121418400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:121409000-121421800	Strong transcription	HSMM	muscle
38	chr3:121410400-121435600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:121410800-121416400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:121410800-121424400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:121411000-121421200	Strong transcription	GM12878-XiMat	blood
42	chr3:121411000-121432000	Weak transcription	NHEK	skin
43	chr3:121411000-121432800	Weak transcription	Fetal Brain Male	brain
44	chr3:121411000-121442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:121411400-121415800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:121411400-121415800	Weak transcription	Thymus	Thymus
47	chr3:121411400-121415800	Weak transcription	A549	lung
48	chr3:121411400-121416200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:121411400-121416200	Weak transcription	HUVEC	blood vessel
50	chr3:121411400-121416400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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