Variant report

Variant	rs12638492
Chromosome Location	chr3:121711763-121711764
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	chr3:121552092..121554395-chr3:121711264..121713360,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173226	Chromatin interaction
ENSG00000145088	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10934565	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12488334	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12488851	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12491991	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493408	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12493952	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12497349	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12498028	0.84[EUR][1000 genomes]
rs12629742	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12630486	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12632345	0.83[EUR][1000 genomes]
rs12637351	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12637968	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13067270	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13083557	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13089878	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13093171	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1344279	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1920290	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920291	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920297	0.82[EUR][1000 genomes]
rs1920298	0.84[EUR][1000 genomes]
rs1920299	0.84[EUR][1000 genomes]
rs1920309	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1986368	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1986712	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2091664	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2332033	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2332035	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2689285	0.83[EUR][1000 genomes]
rs2689290	0.83[EUR][1000 genomes]
rs2877560	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2877561	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34158925	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181646	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34478505	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34543553	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34566912	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34696871	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34837785	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35101693	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35415993	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35737776	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35902163	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3915060	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3942629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4118376	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4285028	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4305455	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4676758	0.81[EUR][1000 genomes]
rs6790281	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71329246	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71329247	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71329249	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73855465	0.83[EUR][1000 genomes]
rs73855476	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73855480	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73855481	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7615571	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7637495	0.83[EUR][1000 genomes]
rs7640872	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651226	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12638492	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs12638492	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs12638492	IQCB1	cis	Esophagus Muscularis	GTEx
rs12638492	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs12638492	ILDR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121699400-121714200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:121704800-121721400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:121705200-121714000	Weak transcription	HMEC	breast
4	chr3:121705200-121729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:121706000-121721200	Weak transcription	Fetal Kidney	kidney
6	chr3:121707000-121714200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:121707400-121711800	Weak transcription	Colonic Mucosa	Colon
8	chr3:121708600-121713400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:121708800-121711800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:121708800-121718000	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:121709000-121713400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:121709000-121713600	Enhancers	Primary B cells from cord blood	blood
13	chr3:121709200-121719200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:121709600-121721800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:121709800-121712600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr3:121709800-121714000	Weak transcription	Lung	lung
17	chr3:121710600-121713600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:121710800-121713200	Weak transcription	HUVEC	blood vessel
19	chr3:121711200-121713000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr3:121711400-121711800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:121711400-121711800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
22	chr3:121711400-121712000	Enhancers	Fetal Muscle Leg	muscle
23	chr3:121711400-121712200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:121711600-121712000	Genic enhancers	Esophagus	oesophagus
25	chr3:121711600-121712400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:121711600-121712400	Genic enhancers	Rectal Mucosa Donor 29	rectum
27	chr3:121711600-121712800	Strong transcription	Fetal Intestine Large	intestine
28	chr3:121711600-121712800	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:121711600-121713800	Strong transcription	Pancreas	Pancrea
30	chr3:121711600-121714000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:121711600-121714000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:121711600-121714800	Strong transcription	Fetal Intestine Small	intestine
33	chr3:121711600-121715000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:121711600-121715400	Enhancers	Spleen	Spleen

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