Variant report

Variant	rs1920320
Chromosome Location	chr3:121547527-121547528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121541912..121545321-chr3:121545405..121548683,3	MCF-7	breast:
2	chr3:121537691..121539463-chr3:121547054..121549794,2	K562	blood:
3	chr3:121547116..121548952-chr3:121552697..121555325,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145088	Chromatin interaction
ENSG00000173226	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11706783	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11707504	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11707518	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714406	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11715951	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717483	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719093	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719458	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11721291	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11721318	0.91[CEU][hapmap]
rs13061326	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13062684	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13065245	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13072767	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083794	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13087578	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13090798	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13098883	0.88[ASN][1000 genomes]
rs1318472	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13433692	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13434284	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1573819	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17691170	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17742508	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2070180	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs28660600	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28674947	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34865234	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35359572	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35679661	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805127	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4280673	0.88[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4298081	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4311252	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4413346	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57636696	0.80[AMR][1000 genomes]
rs6768621	0.96[CEU][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769102	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6776670	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6780302	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6784571	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6789736	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629369	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7649092	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9289177	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812137	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9812228	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9816844	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9822949	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9825248	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9826473	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9839617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841595	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9848027	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856641	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9878086	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9883467	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
8	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv933192	chr3:121544496-121575871	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1920320	IQCB1	cis	Whole Blood	GTEx
rs1920320	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs1920320	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs1920320	HCLS1	cis	Whole Blood	GTEx
rs1920320	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121491600-121552600	Weak transcription	NHLF	lung
2	chr3:121528000-121553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:121530800-121552200	Weak transcription	Small Intestine	intestine
4	chr3:121530800-121552400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:121530800-121552800	Weak transcription	HSMMtube	muscle
6	chr3:121530800-121553000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:121530800-121553200	Weak transcription	Esophagus	oesophagus
8	chr3:121531000-121552800	Weak transcription	Fetal Stomach	stomach
9	chr3:121531000-121552800	Weak transcription	Pancreas	Pancrea
10	chr3:121531000-121552800	Weak transcription	Right Ventricle	heart
11	chr3:121531000-121552800	Weak transcription	Spleen	Spleen
12	chr3:121531200-121549600	Weak transcription	Brain Angular Gyrus	brain
13	chr3:121535400-121551200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:121536000-121551600	Strong transcription	Fetal Thymus	thymus
15	chr3:121536200-121552800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:121536400-121548000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr3:121537200-121552600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:121537400-121552800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:121538400-121552000	Weak transcription	Gastric	stomach
20	chr3:121539600-121548200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:121539800-121548200	Strong transcription	Liver	Liver
22	chr3:121539800-121552600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:121539800-121552600	Strong transcription	HSMM	muscle
24	chr3:121540000-121548200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr3:121540000-121552000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:121540200-121549000	Strong transcription	Placenta	Placenta
27	chr3:121541000-121548200	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:121541200-121553000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:121541400-121548400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:121541400-121552800	Weak transcription	Aorta	Aorta
31	chr3:121541600-121550000	Weak transcription	Psoas Muscle	Psoas
32	chr3:121541600-121552800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:121542200-121552800	Weak transcription	Left Ventricle	heart
34	chr3:121542600-121548000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:121542600-121548800	Strong transcription	NHDF-Ad	bronchial
36	chr3:121542800-121553200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:121543000-121547800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:121543000-121548000	Strong transcription	HUVEC	blood vessel
39	chr3:121543000-121548400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:121543000-121548600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:121543000-121548800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:121543000-121553400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:121543200-121548200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:121543200-121548400	Weak transcription	Thymus	Thymus
45	chr3:121543200-121548600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:121543200-121548800	Strong transcription	Primary B cells from cord blood	blood
47	chr3:121543200-121549600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr3:121543200-121551000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:121543200-121552600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:121543200-121552800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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