Variant report

Variant	rs2292533
Chromosome Location	chr4:76861859-76861860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:172)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:172 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr4:76861857-76862164	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr4:76861805-76862289	K562	blood:	n/a	n/a
3	POLR2A	chr4:76861823-76862315	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr4:76861707-76862432	K562	blood:	n/a	n/a
5	CEBPD	chr4:76861778-76862006	HepG2	liver:	n/a	n/a
6	CHD2	chr4:76861800-76862327	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr4:76861776-76862177	GM12878	blood:	n/a	n/a
8	CEBPB	chr4:76861744-76862072	A549	lung:	n/a	n/a
9	POLR2A	chr4:76861848-76862416	H1-neurons	neurons:	n/a	n/a
10	MTA3	chr4:76861530-76862110	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:76860729-76862379	GM12892	blood:	n/a	n/a
12	GABPA	chr4:76861714-76862451	H1-hESC	embryonic stem cell:	n/a	n/a
13	NR2F2	chr4:76860929-76862406	MCF-7	breast:	n/a	n/a
14	CEBPB	chr4:76861676-76862305	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr4:76861811-76862373	GM12878	blood:	n/a	n/a
16	MXI1	chr4:76860858-76862599	IMR90	lung:	n/a	n/a
17	MAX	chr4:76860853-76862432	HepG2	liver:	n/a	n/a
18	MYC	chr4:76860970-76862320	K562	blood:	n/a	n/a
19	MAX	chr4:76860862-76862474	MCF-7	breast:	n/a	n/a
20	POLR2A	chr4:76861713-76862439	A549	lung:	n/a	n/a
21	POLR2A	chr4:76860996-76862279	Hela-S3	cervix:	n/a	n/a
22	HDAC2	chr4:76861805-76862486	K562	blood:	n/a	n/a
23	POLR2A	chr4:76860943-76862413	GM19193	blood:	n/a	n/a
24	TAF1	chr4:76861516-76862389	HepG2	liver:	n/a	n/a
25	TCF12	chr4:76861494-76862177	A549	lung:	n/a	n/a
26	MAX	chr4:76860764-76862553	HCT-116	colon:	n/a	n/a
27	POLR2A	chr4:76861823-76862310	A549	lung:	n/a	n/a
28	ZKSCAN1	chr4:76861845-76861967	Hela-S3	cervix:	n/a	n/a
29	REST	chr4:76861750-76862194	PFSK-1	brain:	n/a	n/a
30	YY1	chr4:76861805-76861986	K562	blood:	n/a	n/a
31	CEBPB	chr4:76861772-76861955	HepG2	liver:	n/a	n/a
32	YY1	chr4:76861654-76862411	HepG2	liver:	n/a	n/a
33	POLR2A	chr4:76860900-76862382	GM18951	blood:	n/a	n/a
34	POLR2A	chr4:76861852-76862231	A549	lung:	n/a	n/a
35	MAX	chr4:76861833-76862286	K562	blood:	n/a	n/a
36	CEBPB	chr4:76861625-76862243	A549	lung:	n/a	n/a
37	POLR2A	chr4:76860905-76862315	GM19099	blood:	n/a	n/a
38	POLR2A	chr4:76860793-76862484	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr4:76861070-76862374	A549	lung:	n/a	n/a
40	FOXP2	chr4:76861859-76862382	PFSK-1	brain:	n/a	n/a
41	CCNT2	chr4:76861044-76862433	K562	blood:	n/a	n/a
42	MAZ	chr4:76861145-76862403	HepG2	liver:	n/a	n/a
43	HDAC2	chr4:76861716-76862358	HepG2	liver:	n/a	n/a
44	MAX	chr4:76861675-76861973	GM12878	blood:	n/a	n/a
45	POLR2A	chr4:76861775-76862421	HUVEC	blood vessel:	n/a	n/a
46	ELF1	chr4:76860827-76862481	GM12878	blood:	n/a	n/a
47	E2F6	chr4:76861683-76862522	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr4:76860887-76862457	K562	blood:	n/a	n/a
49	CHD1	chr4:76861674-76862205	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr4:76860842-76862484	HL-60	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:76597293..76598968-chr4:76860443..76862946,2	K562	blood:
2	chr4:76861526..76863582-chr4:76870984..76872556,2	K562	blood:
3	chr4:76860117..76861999-chr4:76911234..76914144,3	K562	blood:
4	chr4:76857067..76859381-chr4:76860422..76862398,2	K562	blood:
5	chr4:76861625..76863720-chr4:76909476..76912300,3	MCF-7	breast:
6	chr4:76859621..76862443-chr4:76895909..76899158,3	K562	blood:

No data

Variant related genes	Relation type
NAAA	TF binding region
ENSG00000138757	Chromatin interaction
ENSG00000198301	Chromatin interaction
ENSG00000268788	Chromatin interaction
ENSG00000138744	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10008757	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097189	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11732759	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11931349	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11947509	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13111710	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125558	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13126007	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13132564	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13138223	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2242471	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242473	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242474	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28681066	0.81[ASN][1000 genomes]
rs4282209	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4337760	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859413	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859581	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859582	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532078	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6826085	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7436021	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7679177	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9307050	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9992952	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9995007	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS 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	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv3396277	chr4:76861228-76865426	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2292533	NAAA	cis	Heart Left Ventricle	GTEx
rs2292533	NAAA	cis	Esophagus Muscularis	GTEx
rs2292533	NAAA	cis	Muscle Skeletal	GTEx
rs2292533	NAAA	cis	Adipose Subcutaneous	GTEx
rs2292533	NAAA	cis	lung	GTEx
rs2292533	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs2292533	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs2292533	NAAA	cis	Esophagus Mucosa	GTEx
rs2292533	NAAA	cis	Nerve Tibial	GTEx
rs2292533	NAAA	cis	Artery Aorta	GTEx
rs2292533	ASAHL	cis	multi-tissue	Pritchard
rs2292533	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs2292533	ART3	cis	Nerve Tibial	GTEx
rs2292533	NAAA	cis	Artery Tibial	GTEx
rs2292533	NAAA	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76860400-76862600	Active TSS	A549	lung
2	chr4:76860600-76862000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:76860600-76862400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:76860600-76862600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr4:76860600-76862600	Active TSS	Colonic Mucosa	Colon
6	chr4:76860600-76862600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr4:76860600-76862600	Active TSS	Rectal Smooth Muscle	rectum
8	chr4:76860800-76862000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:76860800-76862000	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr4:76860800-76862000	Active TSS	Fetal Heart	heart
11	chr4:76860800-76862000	Active TSS	Fetal Kidney	kidney
12	chr4:76860800-76862000	Active TSS	Fetal Lung	lung
13	chr4:76860800-76862000	Flanking Active TSS	HMEC	breast
14	chr4:76860800-76862200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr4:76860800-76862200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:76860800-76862200	Active TSS	Placenta Amnion	Placenta Amnion
17	chr4:76860800-76862200	Active TSS	NHDF-Ad	bronchial
18	chr4:76860800-76862400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:76860800-76862400	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr4:76860800-76862400	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr4:76860800-76862400	Active TSS	Brain Angular Gyrus	brain
22	chr4:76860800-76862400	Active TSS	Esophagus	oesophagus
23	chr4:76860800-76862400	Active TSS	Fetal Brain Female	brain
24	chr4:76860800-76862400	Active TSS	Ovary	ovary
25	chr4:76860800-76862400	Active TSS	Right Ventricle	heart
26	chr4:76860800-76862400	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr4:76860800-76862400	Active TSS	Hela-S3	cervix
28	chr4:76860800-76862600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr4:76860800-76862600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:76860800-76862600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr4:76860800-76862600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr4:76860800-76862600	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr4:76860800-76862600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:76860800-76862600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:76860800-76862600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:76860800-76862600	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr4:76860800-76862600	Active TSS	Primary T cells from cord blood	blood
38	chr4:76860800-76862600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:76860800-76862600	Active TSS	Brain Anterior Caudate	brain
40	chr4:76860800-76862600	Active TSS	Brain Cingulate Gyrus	brain
41	chr4:76860800-76862600	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr4:76860800-76862600	Active TSS	Brain Substantia Nigra	brain
43	chr4:76860800-76862600	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr4:76860800-76862600	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr4:76860800-76862600	Active TSS	Psoas Muscle	Psoas
46	chr4:76860800-76862600	Active TSS	K562	blood
47	chr4:76860800-76862600	Active TSS	NHLF	lung
48	chr4:76861000-76862000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:76861000-76862000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr4:76861000-76862000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood

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