Variant report

Variant	rs60154494
Chromosome Location	chr3:121523252-121523253
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121515767..121519449-chr3:121522232..121524436,3	MCF-7	breast:
2	chr3:121522927..121524938-chr3:121541691..121544252,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16845505	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72626328	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72626329	0.96[ASN][1000 genomes]
rs9818226	0.84[EUR][1000 genomes]
rs9854863	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9856046	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861782	0.81[EUR][1000 genomes]
rs9862127	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9863007	0.81[EUR][1000 genomes]
rs9868875	0.84[EUR][1000 genomes]
rs9882312	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884018	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	nsv933676	chr3:121517764-121528304	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv2447293	chr3:121522240-121524036	Strong transcription Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs60154494	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs60154494	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs60154494	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs60154494	GOLGB1	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121486200-121526600	Weak transcription	Stomach Mucosa	stomach
2	chr3:121486800-121532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:121489800-121529800	Weak transcription	Aorta	Aorta
4	chr3:121490000-121529800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:121490000-121529800	Weak transcription	Pancreas	Pancrea
6	chr3:121491600-121552600	Weak transcription	NHLF	lung
7	chr3:121494200-121544200	Weak transcription	Fetal Brain Male	brain
8	chr3:121494400-121530000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:121500200-121524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:121500200-121541400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:121500600-121528200	Weak transcription	Brain Angular Gyrus	brain
12	chr3:121501200-121524000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:121501400-121529800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:121504800-121524000	Weak transcription	Hela-S3	cervix
15	chr3:121505800-121523600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:121506400-121529800	Weak transcription	Fetal Stomach	stomach
17	chr3:121507000-121529800	Weak transcription	Colonic Mucosa	Colon
18	chr3:121507000-121545400	Weak transcription	Fetal Heart	heart
19	chr3:121507200-121536000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:121508000-121523600	Weak transcription	Fetal Brain Female	brain
21	chr3:121508000-121525000	Weak transcription	Thymus	Thymus
22	chr3:121508000-121529800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:121508200-121535800	Weak transcription	Psoas Muscle	Psoas
24	chr3:121508400-121524400	Weak transcription	Left Ventricle	heart
25	chr3:121508400-121524400	Weak transcription	Lung	lung
26	chr3:121508400-121529800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:121508400-121529800	Weak transcription	Esophagus	oesophagus
28	chr3:121508400-121536400	Weak transcription	HUVEC	blood vessel
29	chr3:121508600-121523400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:121508600-121523400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:121508600-121523600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:121508600-121524800	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:121508600-121525000	Weak transcription	Brain Anterior Caudate	brain
34	chr3:121508600-121529600	Weak transcription	Brain Substantia Nigra	brain
35	chr3:121508600-121529800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:121508600-121529800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:121508600-121529800	Weak transcription	NHEK	skin
38	chr3:121508600-121541400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:121508800-121523600	Weak transcription	HMEC	breast
40	chr3:121508800-121524400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:121508800-121525200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:121508800-121530000	Weak transcription	Brain Germinal Matrix	brain
43	chr3:121508800-121530200	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:121509000-121523400	Weak transcription	HepG2	liver
45	chr3:121509000-121523600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:121509000-121523600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:121509000-121524200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:121509000-121524400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:121509000-121524400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:121509000-121524600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links