Variant report

Variant	rs1133328
Chromosome Location	chr3:19987539-19987540
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	POLR2A	chr3:19987362-19989595	K562	blood:	n/a	n/a
2	POLR2A	chr3:19986887-19989909	GM12891	blood:	n/a	n/a
3	SIN3AK20	chr3:19987338-19989938	MCF-7	breast:	n/a	n/a
4	JUN	chr3:19987484-19988866	K562	blood:	n/a	n/a
5	SMARCC1	chr3:19986964-19989766	Hela-S3	cervix:	n/a	chr3:19989188-19989197 chr3:19989189-19989198
6	POLR2A	chr3:19987474-19989718	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:19987476-19989652	U87	brain:	n/a	n/a
8	POLR2A	chr3:19987429-19989814	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBP	chr3:19986938-19989974	K562	blood:	n/a	n/a
10	POLR2A	chr3:19987007-19989845	K562	blood:	n/a	n/a
11	POLR2A	chr3:19986884-19989655	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:19986589-19991063	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr3:19986935-19988000	A549	lung:	n/a	chr3:19987312-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987325 chr3:19987314-19987323
14	GATA1	chr3:19987428-19990353	PBDE	blood:	n/a	chr3:19990147-19990157
15	UBTF	chr3:19987157-19989859	K562	blood:	n/a	n/a
16	MYC	chr3:19986886-19989780	K562	blood:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
17	MAFF	chr3:19986970-19988337	K562	blood:	n/a	n/a
18	ZMIZ1	chr3:19987025-19989940	K562	blood:	n/a	n/a
19	TEAD4	chr3:19987245-19989018	K562	blood:	n/a	n/a
20	CEBPB	chr3:19986878-19988787	K562	blood:	n/a	chr3:19987312-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987325 chr3:19987314-19987323
21	ZNF384	chr3:19986941-19987984	K562	blood:	n/a	n/a
22	TAL1	chr3:19986884-19990195	K562	blood:	n/a	chr3:19989618-19989626
23	POLR2A	chr3:19986679-19989723	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr3:19986941-19989740	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr3:19987449-19987595	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD1	chr3:19987459-19990325	IMR90	lung:	n/a	chr3:19989363-19989373
27	USF2	chr3:19987523-19988716	Hela-S3	cervix:	n/a	chr3:19988614-19988630 chr3:19988464-19988475
28	POLR2A	chr3:19987273-19989684	GM12878	blood:	n/a	n/a
29	UBTF	chr3:19987082-19989813	K562	blood:	n/a	n/a
30	POLR2A	chr3:19987004-19989709	K562	blood:	n/a	n/a
31	POLR2A	chr3:19987098-19989617	GM19099	blood:	n/a	n/a
32	MAX	chr3:19987005-19989658	Hela-S3	cervix:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
33	CEBPB	chr3:19987127-19987856	HepG2	liver:	n/a	chr3:19987312-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987325 chr3:19987314-19987323
34	BHLHE40	chr3:19986568-19989780	K562	blood:	n/a	chr3:19988614-19988630
35	POLR2A	chr3:19987503-19989666	NB4	blood:	n/a	n/a
36	ELK1	chr3:19987425-19989175	K562	blood:	n/a	n/a
37	JUND	chr3:19986575-19989825	K562	blood:	n/a	chr3:19989188-19989197 chr3:19989189-19989198 chr3:19989190-19989201 chr3:19989187-19989199 chr3:19989187-19989198 chr3:19989188-19989198
38	MAX	chr3:19987272-19989451	NB4	blood:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
39	POLR2A	chr3:19986897-19989746	K562	blood:	n/a	n/a
40	PML	chr3:19987372-19989859	K562	blood:	n/a	chr3:19989187-19989196 chr3:19989190-19989199
41	MAX	chr3:19987443-19989620	A549	lung:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
42	RCOR1	chr3:19986981-19989819	K562	blood:	n/a	n/a
43	CHD2	chr3:19987033-19989885	K562	blood:	n/a	chr3:19989363-19989373
44	POLR2A	chr3:19986935-19989740	GM12878	blood:	n/a	n/a
45	GABPA	chr3:19987485-19989772	MCF-7	breast:	n/a	chr3:19987999-19988008 chr3:19988538-19988545
46	TEAD4	chr3:19986933-19989869	K562	blood:	n/a	n/a
47	CEBPB	chr3:19987048-19987643	MCF-7	breast:	n/a	chr3:19987312-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987325 chr3:19987314-19987323
48	POLR2A	chr3:19987089-19989785	Hela-S3	cervix:	n/a	n/a
49	CEBPB	chr3:19986989-19987907	A549	lung:	n/a	chr3:19987312-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987325 chr3:19987314-19987323
50	RCOR1	chr3:19986844-19989796	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:19987528-19987578	U87	brain:	n/a
2	chr3:19987528-19987578	HRCEpiC	kidney:	n/a
3	chr3:19987528-19987578	NH-A	brain:	n/a
4	chr3:19987528-19987578	HCF	heart:	n/a
5	chr3:19987528-19987578	PrEC	prostate:	n/a
6	chr3:19987528-19987578	HNPCEpiC	eye:	n/a
7	chr3:19987528-19987578	LNCaP	prostate:	n/a
8	chr3:19987528-19987578	HRPEpiC	eye:	n/a
9	chr3:19987528-19987578	HCPEpiC	choroid plexus:	n/a
10	chr3:19987528-19987578	MCF10A-Er-Src	breast:	n/a
11	chr3:19987528-19987578	HEK293	kidney:	embryo
12	chr3:19987528-19987578	SK-N-SH	brain:	n/a
13	chr3:19987528-19987578	A549	lung:	n/a
14	chr3:19987528-19987578	HIPEpiC	eye:	n/a
15	chr3:19987528-19987578	AG04450	lung:	fetal
16	chr3:19987528-19987578	HPAEpiC	pulmonary alveolar:	n/a
17	chr3:19987528-19987578	NT2-D1	testis:	n/a
18	chr3:19987528-19987578	BE2_C	brain:	n/a
19	chr3:19987528-19987578	Hela-S3	cervix:	n/a
20	chr3:19987528-19987578	Caco-2	colon:	n/a
21	chr3:19987528-19987578	AoSMC	blood vessel:	n/a
22	chr3:19987528-19987578	HEEpiC	esophagus:	n/a
23	chr3:19987528-19987578	ovcar-3	ovarian:	n/a
24	chr3:19987528-19987578	GM12892	blood:	n/a
25	chr3:19987528-19987578	Jurkat	blood:	n/a
26	chr3:19987528-19987578	GM06990	blood:	n/a
27	chr3:19987528-19987578	GM19239	blood:	n/a
28	chr3:19987528-19987578	NHDF-neo	bronchial:	n/a
29	chr3:19987528-19987578	HRE	kidney:	n/a
30	chr3:19987528-19987578	RPTEC	kidney:	n/a
31	chr3:19987528-19987578	NB4	blood:	n/a
32	chr3:19987528-19987578	Hepatocyte	liver:	n/a
33	chr3:19987528-19987578	HCT-116	colon:	n/a
34	chr3:19987528-19987578	AG09319	gingival:	n/a
35	chr3:19987528-19987578	HMEC	breast:	n/a
36	chr3:19987528-19987578	HepG2	liver:	n/a
37	chr3:19987528-19987578	GM12891	blood:	n/a
38	chr3:19987528-19987578	SK-N-SH_RA	brain:	n/a
39	chr3:19987528-19987578	HAEpiC	amniotic membrane:	n/a
40	chr3:19987528-19987578	T-47D	breast:	n/a
41	chr3:19987528-19987578	GM12878	blood:	n/a
42	chr3:19987528-19987578	K562	blood:	n/a
43	chr3:19987528-19987578	BJ	skin:	n/a
44	chr3:19987528-19987578	SKMC	muscle:	n/a
45	chr3:19987528-19987578	AG10803	skin:	n/a
46	chr3:19987528-19987578	AG04449	skin:	fetal
47	chr3:19987528-19987578	ProgFib	skin:	n/a
48	chr3:19987528-19987578	MCF-7	breast:	n/a
49	chr3:19987528-19987578	HCM	heart:	n/a
50	chr3:19987528-19987578	PFSK-1	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
3	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
4	chr3:19987513..19990087-chr3:20080861..20083140,3	MCF-7	breast:
5	chr3:19985145..19990136-chr3:20225418..20228312,6	K562	blood:
6	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFHB-2	chr3:19987406-19987746	NONHSAT088605

Variant related genes	Relation type
RAB5A	TF binding region
HSPA8P18	TF binding region
RAB5A	CpG island
HSPA8P18	CpG island
ENSG00000129810	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000114166	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11128927	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13097697	1.00[ASN][1000 genomes]
rs4103004	0.92[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs4610240	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs62241278	0.93[ASN][1000 genomes]
rs71316239	1.00[ASN][1000 genomes]
rs7434271	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs1133328	EFHB,LOC100130288	cis	occipital cortex	BrainEAC
rs1133328	EFHB	cis	Nerve Tibial	GTEx
rs1133328	EFHB	cis	Artery Tibial	GTEx
rs1133328	EFHB,LOC100130288	cis	putamen	BrainEAC
rs1133328	EFHB,LOC100130288	cis	thalamus	BrainEAC
rs1133328	EFHB,LOC100130288	cis	cerebellar cortex	BrainEAC
rs1133328	EFHB	cis	parietal	SCAN
rs1133328	EFHB	cis	Artery Aorta	GTEx
rs1133328	EFHB	cis	Adipose Subcutaneous	GTEx
rs1133328	EFHB	cis	Muscle Skeletal	GTEx
rs1133328	EFHB,LOC100130288	cis	temporal cortex	BrainEAC
rs1133328	EFHB	cis	Whole Blood	GTEx
rs1133328	EFHB	cis	Esophagus Muscularis	GTEx
rs1133328	EFHB	cis	cerebellum	SCAN
rs1133328	EFHB,LOC100130288	cis	intralobular white matter	BrainEAC
rs1133328	EFHB	cis	lung	GTEx
rs1133328	EFHB	cis	Thyroid	GTEx
rs1133328	EFHB,LOC100130288	cis	inferior olivary nucleus	BrainEAC
rs1133328	EFHB,LOC100130288	cis	frontal cortex	BrainEAC
rs1133328	EFHB,LOC100130288	cis	brain	BrainEAC
rs1133328	EFHB,LOC100130288	cis	hippocampus	BrainEAC
rs1133328	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs1133328	EFHB	cis	Stomach	GTEx
rs1133328	EFHB	cis	Esophagus Mucosa	GTEx
rs1133328	EFHB,LOC100130288	cis	substantia nigra	BrainEAC

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19979600-19987600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:19979600-19987800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:19983800-19987600	Weak transcription	Aorta	Aorta
4	chr3:19984800-19987600	Weak transcription	Esophagus	oesophagus
5	chr3:19985600-19987600	Weak transcription	Fetal Lung	lung
6	chr3:19986800-19987800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr3:19986800-19988000	Flanking Active TSS	Hela-S3	cervix
8	chr3:19986800-19990200	Active TSS	Duodenum Mucosa	Duodenum
9	chr3:19987000-19987600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:19987000-19987600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:19987000-19987600	Enhancers	Psoas Muscle	Psoas
12	chr3:19987000-19987600	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr3:19987000-19987600	Active TSS	GM12878-XiMat	blood
14	chr3:19987000-19987800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:19987000-19989600	Active TSS	Liver	Liver
16	chr3:19987200-19987600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:19987200-19987600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:19987200-19987600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:19987200-19987600	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:19987200-19987600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr3:19987200-19987600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:19987200-19987600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr3:19987200-19987600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:19987200-19987600	Active TSS	Adipose Nuclei	Adipose
25	chr3:19987200-19987600	Enhancers	HMEC	breast
26	chr3:19987200-19987600	Enhancers	HUVEC	blood vessel
27	chr3:19987200-19987800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:19987200-19987800	Enhancers	Primary hematopoietic stem cells	blood
29	chr3:19987200-19987800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:19987200-19989000	Active TSS	HepG2	liver
31	chr3:19987200-19989800	Active TSS	Pancreas	Pancrea
32	chr3:19987200-19990400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:19987200-19990400	Active TSS	Placenta	Placenta
34	chr3:19987200-19990600	Active TSS	K562	blood
35	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr3:19987400-19987600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:19987400-19987600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:19987400-19987600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:19987400-19987600	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr3:19987400-19987600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr3:19987400-19987600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:19987400-19987600	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr3:19987400-19987600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:19987400-19987600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr3:19987400-19987600	Enhancers	Primary B cells from cord blood	blood
46	chr3:19987400-19987600	Enhancers	Primary T cells from cord blood	blood
47	chr3:19987400-19987600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr3:19987400-19987600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr3:19987400-19987600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:19987400-19987600	Enhancers	Primary T helper cells fromperipheralblood	blood

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