Variant report

Variant	rs12498028
Chromosome Location	chr3:121612816-121612817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10934565	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11923248	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11928871	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12488334	0.84[EUR][1000 genomes]
rs12488851	0.85[EUR][1000 genomes]
rs12491991	0.84[EUR][1000 genomes]
rs12493408	0.85[EUR][1000 genomes]
rs12493952	0.84[EUR][1000 genomes]
rs12496318	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12497349	0.84[EUR][1000 genomes]
rs12629742	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630486	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12632345	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12634032	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12637351	0.85[EUR][1000 genomes]
rs12637968	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12638492	0.84[EUR][1000 genomes]
rs13067270	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13083557	0.85[EUR][1000 genomes]
rs13086277	0.84[AFR][1000 genomes]
rs13089878	0.84[EUR][1000 genomes]
rs1344279	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1920290	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1920291	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1920297	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920298	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1920299	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1920309	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1986368	0.84[EUR][1000 genomes]
rs1986712	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2091664	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2141487	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2332033	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2689285	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2689290	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2877560	0.85[EUR][1000 genomes]
rs34158925	0.85[EUR][1000 genomes]
rs34181646	0.84[EUR][1000 genomes]
rs34478505	0.84[EUR][1000 genomes]
rs34543553	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34566912	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34696871	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34837785	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35101693	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35415993	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35737776	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35902163	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3942629	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4118376	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4285028	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4305455	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4676758	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6790281	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71329246	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71329247	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73855465	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73855476	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73855480	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73855481	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7615571	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7623901	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637495	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7640872	0.82[EUR][1000 genomes]
rs7651226	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9823335	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv877384	chr3:121601577-121659774	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12498028	STAM2	trans	lymphoblastoid	RTeQTL
rs12498028	IQCB1	cis	Esophagus Muscularis	GTEx
rs12498028	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs12498028	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs12498028	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121555800-121615600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:121559200-121613200	Weak transcription	Brain Angular Gyrus	brain
3	chr3:121585000-121613200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:121592800-121646800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:121593000-121615400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:121593000-121632400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:121604600-121613200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:121604600-121613400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:121604600-121613400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:121604800-121613000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:121605200-121613800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:121606000-121613000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:121607800-121613000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:121608000-121613000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:121608000-121613000	Weak transcription	GM12878-XiMat	blood
16	chr3:121608400-121613000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:121610400-121613000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:121610600-121621800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:121611200-121613000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:121611400-121613000	Weak transcription	Primary B cells from cord blood	blood
21	chr3:121612000-121613000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:121612200-121613000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:121612200-121613000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:121612200-121613200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:121612200-121613200	Enhancers	Fetal Muscle Leg	muscle
26	chr3:121612200-121614200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:121612400-121613000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:121612400-121613000	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:121612400-121616000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:121612600-121613000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:121612800-121613200	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr3:121612800-121613400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:121612800-121613400	Enhancers	Pancreas	Pancrea
34	chr3:121612800-121613600	Enhancers	Psoas Muscle	Psoas
35	chr3:121612800-121613800	Enhancers	Placenta	Placenta
36	chr3:121612800-121614000	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr3:121612800-121614800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:121612800-121615000	Active TSS	Fetal Muscle Trunk	muscle

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