Variant report

Variant	rs3942629
Chromosome Location	chr3:121724038-121724039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121722572..121724413-chr3:121727539..121730017,2	MCF-7	breast:
2	chr3:121722157..121724632-chr3:121744396..121746497,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10934565	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12488334	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12488851	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12491991	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12493408	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12493952	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12496318	0.88[GIH][hapmap]
rs12497349	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12498028	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12629742	0.84[EUR][1000 genomes]
rs12630486	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12632345	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12637351	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12637968	0.83[EUR][1000 genomes]
rs12638492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13067270	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13083557	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13086277	1.00[AFR][1000 genomes]
rs13089878	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13093171	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1344279	0.80[EUR][1000 genomes]
rs1523519	0.91[MEX][hapmap]
rs17203439	1.00[LWK][hapmap]
rs1920290	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1920291	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1920297	0.82[EUR][1000 genomes]
rs1920298	0.92[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1920299	0.92[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1920309	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1986368	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1986712	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2091664	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2332033	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2332035	0.80[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2689285	0.82[EUR][1000 genomes]
rs2689290	0.88[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs2877560	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2877561	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34158925	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34181646	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34478505	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34543553	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34566912	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34696871	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34837785	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35101693	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35415993	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35737776	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35902163	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3915060	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4118376	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4285028	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4305455	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4676758	0.81[EUR][1000 genomes]
rs6790281	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71329246	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71329247	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71329249	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73855465	0.82[EUR][1000 genomes]
rs73855476	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73855480	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73855481	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7615571	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7623901	0.88[GIH][hapmap]
rs7637495	0.92[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs7640872	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7651226	0.83[AMR][1000 genomes];0.96[EUR][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
rs3942629	IQCB1	cis	Esophagus Muscularis	GTEx
rs3942629	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs3942629	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs3942629	IQCB1	cis	cerebellum	SCAN
rs3942629	IQCB1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121705200-121729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:121713000-121732200	Weak transcription	Esophagus	oesophagus
3	chr3:121720400-121725800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:121720600-121724400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:121720800-121732200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:121720800-121732200	Weak transcription	Pancreas	Pancrea
7	chr3:121721600-121724600	Flanking Active TSS	GM12878-XiMat	blood
8	chr3:121721600-121725200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:121722000-121732400	Weak transcription	Colonic Mucosa	Colon
10	chr3:121722200-121732200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:121722400-121724600	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:121722400-121725800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:121723000-121724400	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr3:121723200-121724600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:121723200-121725800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:121723200-121731800	Weak transcription	NHEK	skin
17	chr3:121723400-121724200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:121723400-121724200	Enhancers	Lung	lung
19	chr3:121723400-121724400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:121723400-121724400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:121723400-121724400	Enhancers	Fetal Intestine Large	intestine
22	chr3:121723400-121724600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr3:121723400-121724600	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:121723400-121725200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr3:121723400-121726600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:121723600-121724400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:121723600-121724400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:121723600-121724600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:121723600-121725800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:121723800-121724200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:121723800-121724800	Weak transcription	Primary B cells from cord blood	blood
32	chr3:121723800-121728000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:121724000-121724200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:121724000-121724600	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr3:121724000-121724800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:121724000-121724800	Weak transcription	Fetal Intestine Small	intestine
37	chr3:121724000-121725000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:121724000-121728600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:121724000-121731800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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