Variant report

Variant	rs1920299
Chromosome Location	chr3:121593769-121593770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10934565	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1127412	1.00[CEU][hapmap]
rs11923248	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11928871	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12488334	0.84[EUR][1000 genomes]
rs12488851	0.92[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs12491991	0.84[EUR][1000 genomes]
rs12493408	0.84[EUR][1000 genomes]
rs12493952	0.83[EUR][1000 genomes]
rs12496318	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12497349	0.83[EUR][1000 genomes]
rs12498028	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12629742	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12630486	0.84[EUR][1000 genomes]
rs12632345	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12634032	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637351	0.84[EUR][1000 genomes]
rs12637968	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12638492	0.84[EUR][1000 genomes]
rs13067270	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13083557	0.92[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs13089878	0.84[EUR][1000 genomes]
rs1344279	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1463736	1.00[CEU][hapmap]
rs1523519	0.86[MEX][hapmap]
rs1574133	1.00[CEU][hapmap]
rs1920290	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1920291	0.83[EUR][1000 genomes]
rs1920297	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1920298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920309	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1986368	0.84[EUR][1000 genomes]
rs1986712	0.81[EUR][1000 genomes]
rs2091664	0.84[EUR][1000 genomes]
rs2141487	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2332033	0.84[EUR][1000 genomes]
rs2332035	0.82[TSI][hapmap]
rs2689285	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2689290	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2877560	0.84[EUR][1000 genomes]
rs2877561	0.84[TSI][hapmap]
rs34158925	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34181646	0.84[EUR][1000 genomes]
rs34478505	0.84[EUR][1000 genomes]
rs34543553	0.84[EUR][1000 genomes]
rs34566912	0.84[EUR][1000 genomes]
rs34696871	0.86[EUR][1000 genomes]
rs34837785	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35101693	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35415993	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35737776	0.84[EUR][1000 genomes]
rs35902163	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3732407	1.00[CEU][hapmap]
rs3732410	1.00[CEU][hapmap]
rs3942629	0.92[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs4118376	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4285028	0.96[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4305455	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4676758	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6771068	1.00[CEU][hapmap];0.88[ASN][1000 genomes]
rs6775822	0.86[ASN][1000 genomes]
rs6790281	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71329246	0.84[EUR][1000 genomes]
rs71329247	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73855465	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73855476	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73855480	0.84[EUR][1000 genomes]
rs73855481	0.84[EUR][1000 genomes]
rs7615571	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7623901	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7640872	0.81[EUR][1000 genomes]
rs7651226	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9823335	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1920299	SLC15A2	cis	cerebellum	SCAN
rs1920299	CCDC37	cis	parietal	SCAN
rs1920299	EAF2	cis	multi-tissue	Pritchard
rs1920299	IQCB1	cis	Esophagus Muscularis	GTEx
rs1920299	IQCB1	cis	cerebellum	SCAN
rs1920299	IQCB1	cis	parietal	SCAN
rs1920299	EAF2	cis	cerebellum	SCAN
rs1920299	GOLGB1	cis	multi-tissue	Pritchard
rs1920299	IQCB1	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121554800-121604000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:121555600-121593800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:121555800-121615600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:121559200-121613200	Weak transcription	Brain Angular Gyrus	brain
5	chr3:121571400-121604200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:121583200-121597600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:121583400-121612400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:121585000-121607600	Weak transcription	Aorta	Aorta
9	chr3:121585000-121613200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:121589600-121602600	Weak transcription	Fetal Lung	lung
11	chr3:121590600-121597800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:121591000-121594000	Weak transcription	Fetal Intestine Large	intestine
13	chr3:121591400-121593800	Strong transcription	Primary hematopoietic stem cells	blood
14	chr3:121591400-121595200	Strong transcription	Primary B cells from cord blood	blood
15	chr3:121591400-121595200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:121591400-121595200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:121591400-121597000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:121591400-121597200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:121591400-121597400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:121591400-121601600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:121592400-121594000	Weak transcription	Adipose Nuclei	Adipose
22	chr3:121592400-121594000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:121592400-121594200	Weak transcription	GM12878-XiMat	blood
24	chr3:121592800-121594400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:121592800-121646800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:121593000-121604000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:121593000-121615400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:121593000-121632400	Weak transcription	Duodenum Mucosa	Duodenum

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