Variant report

Variant	rs3819325
Chromosome Location	chr3:49843723-49843724
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	ELF1	chr3:49843614-49844075	K562	blood:	n/a	n/a
2	RUNX3	chr3:49843452-49844095	GM12878	blood:	n/a	n/a
3	EGR1	chr3:49843720-49843992	GM12878	blood:	n/a	chr3:49843860-49843874 chr3:49843859-49843872 chr3:49843858-49843873 chr3:49843754-49843767
4	POLR2A	chr3:49842536-49844314	HL-60	blood:	n/a	n/a
5	POLR2A	chr3:49843719-49844190	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:49843696-49844099	GM12878	blood:	n/a	n/a
7	RCOR1	chr3:49843395-49844057	K562	blood:	n/a	n/a
8	POLR2A	chr3:49843152-49844326	K562	blood:	n/a	n/a
9	GABPA	chr3:49843704-49844043	K562	blood:	n/a	n/a
10	MAX	chr3:49843647-49844049	K562	blood:	n/a	n/a
11	PML	chr3:49842355-49844573	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:49843717-49844380	K562	blood:	n/a	n/a
13	POLR2A	chr3:49840564-49844844	GM12892	blood:	n/a	n/a
14	ETS1	chr3:49843712-49844070	GM12878	blood:	n/a	chr3:49843945-49843958 chr3:49843955-49843970 chr3:49843724-49843735
15	EP300	chr3:49843503-49844108	GM12878	blood:	n/a	n/a
16	EP300	chr3:49843707-49844131	K562	blood:	n/a	n/a
17	POLR2A	chr3:49839914-49845521	HUVEC	blood vessel:	n/a	n/a
18	SP1	chr3:49843695-49844036	GM12878	blood:	n/a	chr3:49843941-49843955 chr3:49843752-49843766 chr3:49843759-49843768 chr3:49843757-49843769 chr3:49843725-49843739
19	REST	chr3:49843716-49844000	K562	blood:	n/a	n/a
20	TEAD4	chr3:49843647-49844160	K562	blood:	n/a	n/a
21	POLR2A	chr3:49843597-49844084	HUVEC	blood vessel:	n/a	n/a
22	ATF2	chr3:49843680-49844067	GM12878	blood:	n/a	n/a
23	EP300	chr3:49843716-49843975	SK-N-SH_RA	brain:	n/a	n/a
24	POLR2A	chr3:49840600-49844841	GM12878	blood:	n/a	n/a
25	ELF1	chr3:49843636-49844143	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:49843714-49844123	GM12878	blood:	n/a	n/a
27	USF1	chr3:49843695-49843954	SK-N-SH_RA	brain:	n/a	chr3:49843829-49843840
28	MAZ	chr3:49843559-49844078	IMR90	lung:	n/a	n/a
29	POLR2A	chr3:49840052-49844784	HL-60	blood:	n/a	n/a
30	USF1	chr3:49843681-49843923	H1-hESC	embryonic stem cell:	n/a	chr3:49843829-49843840
31	ZBTB7A	chr3:49843599-49844205	K562	blood:	n/a	n/a
32	RCOR1	chr3:49843720-49844112	GM12878	blood:	n/a	n/a
33	MAZ	chr3:49843358-49844119	K562	blood:	n/a	n/a
34	POLR2A	chr3:49843568-49844073	K562	blood:	n/a	n/a
35	YY1	chr3:49843713-49844014	K562	blood:	n/a	n/a
36	POLR2A	chr3:49842242-49845414	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr3:49842141-49845240	HUVEC	blood vessel:	n/a	n/a
38	BCLAF1	chr3:49843564-49844049	GM12878	blood:	n/a	n/a
39	MYC	chr3:49843708-49843981	K562	blood:	n/a	n/a
40	POLR2A	chr3:49843650-49844763	GM12892	blood:	n/a	n/a
41	POLR2A	chr3:49843708-49844070	GM12891	blood:	n/a	n/a
42	POLR2A	chr3:49843703-49844208	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr3:49843094-49844859	K562	blood:	n/a	n/a
44	POLR2A	chr3:49840031-49844843	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:49843637-49844205	SK-N-MC	brain:	n/a	n/a
46	CHD2	chr3:49842705-49843987	GM12878	blood:	n/a	chr3:49843725-49843735
47	POLR2A	chr3:49843714-49844088	K562	blood:	n/a	n/a
48	EBF1	chr3:49843720-49844076	GM12878	blood:	n/a	n/a
49	ZBTB7A	chr3:49843647-49844147	K562	blood:	n/a	n/a
50	MAZ	chr3:49842679-49844058	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:100315142..100315868-chr3:49843571..49844336,2	NB4	blood:
2	chr3:49842643..49844250-chr3:49847224..49849823,3	MCF-7	breast:
3	chr3:49842273..49844588-chr3:49866434..49868538,2	K562	blood:

Variant related genes	Relation type
MIR5193	TF binding region
UBA7	TF binding region
ENSG00000183763	Chromatin interaction
ENSG00000182179	Chromatin interaction
ENSG00000162688	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10049413	0.89[ASN][1000 genomes]
rs1049256	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865958	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10865959	0.89[ASN][1000 genomes]
rs11130214	0.81[ASN][1000 genomes]
rs11130216	0.81[ASN][1000 genomes]
rs11130218	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130219	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130221	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1128535	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11709680	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11710675	0.84[ASN][1000 genomes]
rs11714957	0.84[ASN][1000 genomes]
rs11715304	0.91[ASN][1000 genomes]
rs11716575	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11717256	0.93[ASN][1000 genomes]
rs11717463	0.84[ASN][1000 genomes]
rs11920900	0.82[ASN][1000 genomes]
rs12381242	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490656	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13063621	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13084243	0.84[ASN][1000 genomes]
rs13085679	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13086130	0.84[ASN][1000 genomes]
rs13086465	0.81[ASN][1000 genomes]
rs1317140	0.83[ASN][1000 genomes]
rs13316065	0.88[ASN][1000 genomes]
rs1491986	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1799843	0.90[ASN][1000 genomes]
rs1799845	0.90[ASN][1000 genomes]
rs2234385	0.90[ASN][1000 genomes]
rs2234391	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246832	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2247036	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271960	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271961	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276864	0.89[ASN][1000 genomes]
rs2291542	0.84[ASN][1000 genomes]
rs2307021	0.84[ASN][1000 genomes]
rs2352967	0.88[ASN][1000 genomes]
rs2352974	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2352975	0.89[ASN][1000 genomes]
rs34451146	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34522271	0.84[ASN][1000 genomes]
rs34614773	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34735338	0.84[ASN][1000 genomes]
rs35210174	0.84[ASN][1000 genomes]
rs35261599	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35474403	0.84[ASN][1000 genomes]
rs3749237	0.84[ASN][1000 genomes]
rs3749240	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3749241	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3811695	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3811696	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4519692	0.83[ASN][1000 genomes]
rs4768	0.84[ASN][1000 genomes]
rs4855841	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4855850	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855862	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855867	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57648519	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60205400	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62260715	0.84[ASN][1000 genomes]
rs62260719	0.90[ASN][1000 genomes]
rs62260729	0.89[ASN][1000 genomes]
rs6446295	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6766836	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6775384	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6785549	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6802890	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6804655	0.81[ASN][1000 genomes]
rs695238	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7372725	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7372730	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7372966	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7374183	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7374277	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7426497	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7429353	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7431078	0.84[ASN][1000 genomes]
rs7431106	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7618501	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7618519	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7629936	0.87[ASN][1000 genomes]
rs7634886	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7634902	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7645061	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7648987	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7649348	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814765	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9815766	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9819511	0.87[ASN][1000 genomes]
rs9850465	0.94[ASN][1000 genomes]
rs9853458	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9855505	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9859153	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9865480	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9871654	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9872864	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9873183	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9876508	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9882639	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3819325	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs3819325	RBM6	cis	Thyroid	GTEx
rs3819325	UBA7	cis	Esophagus Mucosa	GTEx
rs3819325	RBM6	cis	Artery Tibial	GTEx
rs3819325	RBM6	cis	Nerve Tibial	GTEx
rs3819325	FAM212A	cis	Esophagus Mucosa	GTEx
rs3819325	UBA7	cis	Whole Blood	GTEx
rs3819325	RBM6	cis	Whole Blood	GTEx
rs3819325	RBM6	cis	lung	GTEx
rs3819325	RBM6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49841000-49845000	Enhancers	Liver	Liver
2	chr3:49841400-49844200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
3	chr3:49841400-49845200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:49841400-49845800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
5	chr3:49841400-49845800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr3:49841400-49846400	Weak transcription	Ovary	ovary
7	chr3:49841400-49847000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:49841600-49844000	Enhancers	Primary T cells from cord blood	blood
9	chr3:49841600-49844000	Enhancers	Fetal Brain Male	brain
10	chr3:49841600-49844400	Enhancers	NH-A	brain
11	chr3:49841600-49845000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:49841600-49845400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr3:49841600-49845600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:49841600-49845800	Enhancers	Dnd41	blood
15	chr3:49841600-49846000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:49841600-49846200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:49841600-49850400	Weak transcription	Small Intestine	intestine
18	chr3:49841800-49844000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:49841800-49844000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:49841800-49844000	Enhancers	NHDF-Ad	bronchial
21	chr3:49841800-49844200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:49841800-49844400	Weak transcription	Gastric	stomach
23	chr3:49841800-49844400	Enhancers	Spleen	Spleen
24	chr3:49841800-49844600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:49841800-49844800	Enhancers	Stomach Mucosa	stomach
26	chr3:49841800-49845400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr3:49841800-49845400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr3:49841800-49845600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:49841800-49845600	Enhancers	Left Ventricle	heart
30	chr3:49841800-49845800	Enhancers	Right Atrium	heart
31	chr3:49842000-49845800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:49842000-49845800	Enhancers	Right Ventricle	heart
33	chr3:49842000-49850600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:49842200-49844800	Enhancers	Brain Anterior Caudate	brain
35	chr3:49842200-49845600	Enhancers	Lung	lung
36	chr3:49842200-49846600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr3:49842400-49844800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:49842600-49844200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr3:49842600-49844200	Weak transcription	Brain Substantia Nigra	brain
40	chr3:49842600-49845200	Enhancers	H9 Cell Line	embryonic stem cell
41	chr3:49842600-49845400	Enhancers	NHLF	lung
42	chr3:49842600-49845600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr3:49842600-49846000	Enhancers	NHEK	skin
44	chr3:49842800-49843800	Enhancers	HMEC	breast
45	chr3:49842800-49844000	Enhancers	Fetal Thymus	thymus
46	chr3:49842800-49844200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:49842800-49844400	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr3:49842800-49844800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:49842800-49845200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr3:49842800-49845200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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