Variant report

Variant	rs1573819
Chromosome Location	chr3:121469646-121469647
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr3:121467515-121469850	SK-N-SH	brain:	n/a	chr3:121468710-121468719 chr3:121468652-121468669 chr3:121468653-121468668 chr3:121468629-121468638 chr3:121468653-121468668
2	POLR2A	chr3:121466284-121469653	IMR90	lung:	n/a	n/a
3	RFX5	chr3:121467360-121469816	IMR90	lung:	n/a	chr3:121468710-121468719 chr3:121468652-121468669 chr3:121468653-121468668 chr3:121468629-121468638 chr3:121468653-121468668
4	POLR2A	chr3:121467827-121469699	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:121466038-121469751	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:121467877-121469673	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:121468824..121470576-chr3:121473102..121475078,2	K562	blood:
2	chr3:121442817..121449533-chr3:121463247..121470201,7	K562	blood:
3	chr3:121465631..121470383-chr3:122100201..122104501,4	MCF-7	breast:
4	chr3:121468842..121470508-chr3:121478422..121481372,2	MCF-7	breast:
5	chr3:121469093..121470860-chr3:121480115..121482218,2	K562	blood:
6	chr3:121263260..121265570-chr3:121468289..121470216,2	K562	blood:
7	chr3:121449263..121451677-chr3:121468938..121471042,2	K562	blood:
8	chr3:121457664..121460185-chr3:121469014..121471399,2	MCF-7	breast:
9	chr3:121261975..121264944-chr3:121467360..121470216,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EAF2-3	chr3:121468132-121470030	NONHSAT091480

Variant related genes	Relation type
GOLGB1	TF binding region
ENSG00000114023	Chromatin interaction
ENSG00000160124	Chromatin interaction
ENSG00000051341	Chromatin interaction
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11706783	0.85[ASN][1000 genomes]
rs11707504	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11707518	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11707716	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714406	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715951	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11716984	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11717483	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11719093	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11719458	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720859	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11721291	0.80[AMR][1000 genomes]
rs11721318	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13061326	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13062684	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13065245	0.80[AMR][1000 genomes]
rs13072618	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13072767	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13074834	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13077135	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13083794	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13087578	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13090798	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1318472	0.80[AMR][1000 genomes]
rs13433692	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13434284	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17691170	0.82[EUR][1000 genomes]
rs17742508	0.80[AMR][1000 genomes]
rs1920320	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2070180	0.82[EUR][1000 genomes]
rs28660600	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28674947	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33988592	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34086988	0.82[EUR][1000 genomes]
rs34667636	0.82[EUR][1000 genomes]
rs34865234	0.80[AMR][1000 genomes]
rs35359572	0.80[AMR][1000 genomes]
rs35679661	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35988617	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36142735	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3732408	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3805127	0.80[AMR][1000 genomes]
rs4280673	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4298081	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4311252	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4413346	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55643643	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55657471	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56314138	0.81[EUR][1000 genomes]
rs62268732	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62268734	0.85[ASN][1000 genomes]
rs66653099	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6768621	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6776670	0.85[ASN][1000 genomes]
rs6784571	0.85[ASN][1000 genomes]
rs6789736	0.85[ASN][1000 genomes]
rs6791046	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7427165	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7629369	0.80[AMR][1000 genomes]
rs7649092	0.80[AMR][1000 genomes]
rs9289177	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9812137	0.82[ASN][1000 genomes]
rs9812228	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9816844	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9822949	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9825248	0.80[AMR][1000 genomes]
rs9826473	0.80[AMR][1000 genomes]
rs9839617	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9841595	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848027	0.81[ASN][1000 genomes]
rs9856641	0.80[AMR][1000 genomes]
rs9878086	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9883467	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1573819	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs1573819	HCLS1	cis	Whole Blood	GTEx
rs1573819	IQCB1	cis	Whole Blood	GTEx
rs1573819	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs1573819	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121466800-121469800	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr3:121466800-121469800	Active TSS	K562	blood
3	chr3:121467000-121469800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:121467000-121469800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr3:121467000-121469800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:121467000-121469800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:121467000-121469800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:121467200-121469800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:121467400-121469800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr3:121467400-121469800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:121467600-121469800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:121467600-121469800	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr3:121468800-121469800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:121469000-121469800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr3:121469000-121469800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr3:121469000-121469800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:121469000-121469800	Flanking Active TSS	Liver	Liver
18	chr3:121469000-121469800	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr3:121469000-121469800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr3:121469200-121469800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:121469200-121469800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:121469200-121469800	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr3:121469200-121469800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr3:121469200-121469800	Flanking Active TSS	Fetal Kidney	kidney
25	chr3:121469200-121469800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr3:121469200-121469800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr3:121469200-121469800	Flanking Active TSS	Dnd41	blood
28	chr3:121469200-121469800	Flanking Active TSS	GM12878-XiMat	blood
29	chr3:121469200-121469800	Flanking Active TSS	Hela-S3	cervix
30	chr3:121469200-121469800	Flanking Active TSS	NHEK	skin
31	chr3:121469200-121469800	Flanking Active TSS	NHLF	lung
32	chr3:121469200-121469800	Flanking Active TSS	Osteobl	bone
33	chr3:121469400-121469800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:121469400-121469800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr3:121469400-121469800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:121469400-121469800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:121469400-121469800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:121469400-121469800	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr3:121469400-121469800	Enhancers	Primary B cells from peripheral blood	blood
40	chr3:121469400-121469800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:121469400-121469800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:121469400-121469800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr3:121469400-121469800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:121469400-121469800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr3:121469400-121469800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:121469400-121469800	Enhancers	Colon Smooth Muscle	Colon
47	chr3:121469400-121469800	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr3:121469400-121469800	Enhancers	Fetal Muscle Leg	muscle
49	chr3:121469400-121469800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr3:121469400-121469800	Enhancers	Small Intestine	intestine

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