Variant report

Variant	rs13062684
Chromosome Location	chr3:121489893-121489894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EAF2-2	chr3:121489799-121490825	l_2448_chr3:121487690-121490825_testes

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11706783	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707504	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715951	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716984	0.80[EUR][1000 genomes]
rs11717483	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721291	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11721318	0.82[EUR][1000 genomes]
rs13061326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065245	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13072618	0.81[EUR][1000 genomes]
rs13072767	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074834	0.82[EUR][1000 genomes]
rs13083794	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13087578	0.80[EUR][1000 genomes]
rs13090798	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098883	0.92[ASN][1000 genomes]
rs1318472	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13433692	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434284	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573819	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17742508	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1920320	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28660600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28674947	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33988592	0.82[EUR][1000 genomes]
rs34865234	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35359572	0.93[AMR][1000 genomes]
rs35679661	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35988617	0.82[EUR][1000 genomes]
rs3732408	0.82[EUR][1000 genomes]
rs3805127	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4280673	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298081	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4311252	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413346	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55643643	0.81[EUR][1000 genomes]
rs55657471	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57636696	0.82[AMR][1000 genomes]
rs6768621	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769102	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6776670	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780302	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784571	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789736	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629369	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7649092	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9289177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812137	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812228	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816844	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9822949	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825248	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9826473	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9839617	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841595	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848027	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9856641	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9878086	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883467	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	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
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv933820	chr3:121489302-121500759	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13062684	IQCB1	cis	Whole Blood	GTEx
rs13062684	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs13062684	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs13062684	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121477200-121494000	Weak transcription	Right Ventricle	heart
2	chr3:121478000-121499400	Weak transcription	HepG2	liver
3	chr3:121483200-121490600	Weak transcription	A549	lung
4	chr3:121483600-121498600	Weak transcription	Fetal Kidney	kidney
5	chr3:121483800-121498400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:121484400-121490600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:121484400-121494000	Weak transcription	Brain Angular Gyrus	brain
8	chr3:121484600-121499000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:121485200-121491000	Weak transcription	HUVEC	blood vessel
10	chr3:121485400-121493200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:121485600-121497200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:121485600-121503200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:121485800-121501000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr3:121486000-121491400	Weak transcription	NHLF	lung
15	chr3:121486200-121491200	Weak transcription	NHEK	skin
16	chr3:121486200-121526600	Weak transcription	Stomach Mucosa	stomach
17	chr3:121486800-121496000	Weak transcription	Hela-S3	cervix
18	chr3:121486800-121532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:121487000-121494000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:121487000-121498800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:121487000-121509000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:121487200-121501600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:121487400-121490000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:121487400-121491600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:121487400-121491600	Strong transcription	NHDF-Ad	bronchial
26	chr3:121487400-121492000	Strong transcription	Adipose Nuclei	Adipose
27	chr3:121487400-121492600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:121487400-121493000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:121487400-121493400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:121487400-121494200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:121487400-121494800	Strong transcription	HSMM	muscle
32	chr3:121487400-121495200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:121487400-121497200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:121487400-121499200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:121487400-121501400	Strong transcription	Primary T cells from cord blood	blood
36	chr3:121487400-121501400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:121487400-121502000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:121487400-121503000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:121487400-121512200	Strong transcription	Fetal Thymus	thymus
40	chr3:121487400-121512400	Strong transcription	Dnd41	blood
41	chr3:121487600-121495600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr3:121487600-121497200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:121487600-121498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:121487800-121491600	Strong transcription	Placenta	Placenta
45	chr3:121487800-121497600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:121487800-121509000	Strong transcription	Fetal Intestine Large	intestine
47	chr3:121487800-121516400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:121487800-121519000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:121488000-121491000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:121488000-121492000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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