Variant report

Variant	rs1574115
Chromosome Location	chr3:121469225-121469226
allele	A/G
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	MXI1	chr3:121467696-121469298	HepG2	liver:	n/a	chr3:121468654-121468669
2	TAF1	chr3:121468102-121469287	A549	lung:	n/a	n/a
3	POLR2A	chr3:121467899-121469277	U87	brain:	n/a	n/a
4	MAZ	chr3:121467960-121469271	K562	blood:	n/a	chr3:121468525-121468533
5	POLR2A	chr3:121467820-121469228	HL-60	blood:	n/a	n/a
6	MAX	chr3:121468060-121469380	GM12878	blood:	n/a	chr3:121468525-121468533
7	NR2C2	chr3:121468112-121469376	GM12878	blood:	n/a	chr3:121468803-121468812
8	POLR2A	chr3:121467550-121469430	GM12878	blood:	n/a	n/a
9	STAT5A	chr3:121468732-121469277	GM12878	blood:	n/a	chr3:121468826-121468838 chr3:121468854-121468862
10	SIN3AK20	chr3:121467623-121469322	MCF-7	breast:	n/a	n/a
11	SP1	chr3:121467781-121469254	HCT-116	colon:	n/a	chr3:121468358-121468370 chr3:121468355-121468369 chr3:121468208-121468217 chr3:121468360-121468369 chr3:121468627-121468648
12	USF2	chr3:121468595-121469564	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:121466904-121469379	Hela-S3	cervix:	n/a	n/a
14	MTA3	chr3:121467953-121469388	GM12878	blood:	n/a	n/a
15	GTF2F1	chr3:121467982-121469471	Hela-S3	cervix:	n/a	n/a
16	SIX5	chr3:121468431-121469284	A549	lung:	n/a	n/a
17	POLR2A	chr3:121467723-121469318	Hela-S3	cervix:	n/a	n/a
18	TCF12	chr3:121467887-121469269	A549	lung:	n/a	chr3:121468503-121468513
19	POLR2A	chr3:121467979-121469263	GM19099	blood:	n/a	n/a
20	SP1	chr3:121467733-121469231	HCT-116	colon:	n/a	chr3:121468358-121468370 chr3:121468355-121468369 chr3:121468208-121468217 chr3:121468360-121468369 chr3:121468627-121468648
21	MXI1	chr3:121467560-121469412	SK-N-SH	brain:	n/a	chr3:121468654-121468669
22	MXI1	chr3:121467777-121469634	IMR90	lung:	n/a	chr3:121468654-121468669
23	MAZ	chr3:121467246-121469293	IMR90	lung:	n/a	chr3:121468525-121468533
24	GABPA	chr3:121467798-121469571	A549	lung:	n/a	n/a
25	CHD2	chr3:121468044-121469255	HepG2	liver:	n/a	chr3:121468365-121468375
26	POLR2A	chr3:121467902-121469246	GM12892	blood:	n/a	n/a
27	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
28	REST	chr3:121467586-121469606	H1-neurons	neurons:	n/a	chr3:121468393-121468406 chr3:121468400-121468410
29	WRNIP1	chr3:121468252-121469463	GM12878	blood:	n/a	n/a
30	GABPA	chr3:121468073-121469332	A549	lung:	n/a	n/a
31	POLR2A	chr3:121467036-121469449	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:121467732-121469390	PBDE	blood:	n/a	n/a
33	POLR2A	chr3:121467771-121469447	GM12878	blood:	n/a	n/a
34	GABPA	chr3:121467591-121469255	MCF-7	breast:	n/a	n/a
35	PML	chr3:121468216-121469274	K562	blood:	n/a	n/a
36	POLR2A	chr3:121467293-121469486	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr3:121466284-121469653	IMR90	lung:	n/a	n/a
38	POLR2A	chr3:121467969-121469341	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr3:121467814-121469282	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr3:121468074-121469277	K562	blood:	n/a	n/a
41	RFX5	chr3:121467360-121469816	IMR90	lung:	n/a	chr3:121468710-121468719 chr3:121468652-121468669 chr3:121468653-121468668 chr3:121468629-121468638 chr3:121468653-121468668
42	NR2C2	chr3:121468095-121469299	Hela-S3	cervix:	n/a	chr3:121468803-121468812
43	SMC3	chr3:121467967-121469402	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:121468103-121469236	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr3:121467684-121469234	MCF-7	breast:	n/a	n/a
46	POLR2A	chr3:121467954-121469302	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr3:121467929-121469227	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr3:121467983-121469423	Raji	blood:	n/a	n/a
49	POLR2A	chr3:121467917-121469244	GM12892	blood:	n/a	n/a
50	POLR2A	chr3:121466257-121469581	MCF10A-Er-Src	breast:	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	chr1:16840308..16841073-chr3:121468270..121469262,2	HCT-116	colon:
6	chr3:48672419..48673115-chr3:121468693..121469249,2	NB4	blood:
7	chr3:121469093..121470860-chr3:121480115..121482218,2	K562	blood:
8	chr3:121263260..121265570-chr3:121468289..121470216,2	K562	blood:
9	chr3:121449263..121451677-chr3:121468938..121471042,2	K562	blood:
10	chr3:121457664..121460185-chr3:121469014..121471399,2	MCF-7	breast:
11	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
ENSG00000206652	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000160124	Chromatin interaction
ENSG00000114023	Chromatin interaction
ENSG00000173230	Chromatin interaction
ENSG00000051341	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10049060	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1127412	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11916169	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11928871	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12634032	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12635865	0.86[EUR][1000 genomes]
rs1463736	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1574133	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2141487	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3732407	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732410	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3772126	0.81[EUR][1000 genomes]
rs4048699	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4048703	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58367397	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6771068	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6775822	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6791882	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7153	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7610298	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7623901	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7647351	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7648340	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7648343	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9808981	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9817818	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9818073	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9820511	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9823335	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9824235	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9824760	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9838301	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9850439	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9852845	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9874722	0.91[AMR][1000 genomes];0.89[EUR][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
rs1574115	STAM2	trans	lymphoblastoid	RTeQTL
rs1574115	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs1574115	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs1574115	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs1574115	IQCB1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121466400-121469600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:121466400-121469600	Active TSS	Right Atrium	heart
3	chr3:121466600-121469400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:121466800-121469400	Active TSS	Fetal Intestine Small	intestine
5	chr3:121466800-121469600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:121466800-121469600	Active TSS	Psoas Muscle	Psoas
7	chr3:121466800-121469800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr3:121466800-121469800	Active TSS	K562	blood
9	chr3:121467000-121469400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:121467000-121469800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:121467000-121469800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr3:121467000-121469800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:121467000-121469800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:121467000-121469800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:121467200-121469400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:121467200-121469400	Active TSS	Fetal Intestine Large	intestine
17	chr3:121467200-121469400	Active TSS	Stomach Mucosa	stomach
18	chr3:121467200-121469800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:121467400-121469400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:121467400-121469400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:121467400-121469400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:121467400-121469400	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr3:121467400-121469400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:121467400-121469400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:121467400-121469400	Active TSS	Fetal Muscle Trunk	muscle
26	chr3:121467400-121469400	Active TSS	Gastric	stomach
27	chr3:121467400-121469400	Bivalent/Poised TSS	HepG2	liver
28	chr3:121467400-121469600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:121467400-121469600	Active TSS	Esophagus	oesophagus
30	chr3:121467400-121469600	Active TSS	Left Ventricle	heart
31	chr3:121467400-121469800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr3:121467400-121469800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:121467600-121469400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:121467600-121469600	Active TSS	Colonic Mucosa	Colon
35	chr3:121467600-121469800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:121467600-121469800	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr3:121467800-121469600	Active TSS	Rectal Smooth Muscle	rectum
38	chr3:121468400-121469400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:121468600-121469400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:121468800-121469400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr3:121468800-121469400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:121468800-121469600	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr3:121468800-121469600	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr3:121468800-121469600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr3:121468800-121469600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:121468800-121469800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:121469000-121469400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr3:121469000-121469400	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr3:121469000-121469400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:121469000-121469400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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