Variant report

Variant	rs1530799
Chromosome Location	chr4:121844422-121844423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr4:121843888-121844425	H1-hESC	embryonic stem cell:	n/a	chr4:121844050-121844059
2	MAX	chr4:121843533-121844478	ECC-1	luminal epithelium:	n/a	n/a
3	TAF1	chr4:121843044-121844472	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:121842695-121844484	U87	brain:	n/a	n/a
5	POLR2A	chr4:121844103-121844537	H1-neurons	neurons:	n/a	n/a
6	KAP1	chr4:121843958-121844544	U2OS	brain:	n/a	n/a
7	MAX	chr4:121842609-121844629	A549	lung:	n/a	chr4:121843282-121843291 chr4:121843446-121843456
8	POLR2A	chr4:121843589-121844452	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAZ	chr4:121842884-121844814	IMR90	lung:	n/a	chr4:121843282-121843291 chr4:121843446-121843456
10	TCF12	chr4:121844002-121844483	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr4:121842458-121844689	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF12	chr4:121843045-121844473	ECC-1	luminal epithelium:	n/a	n/a
13	SP1	chr4:121843663-121844589	H1-hESC	embryonic stem cell:	n/a	chr4:121844039-121844060 chr4:121843900-121843914 chr4:121843940-121843954
14	SP1	chr4:121843722-121844576	H1-hESC	embryonic stem cell:	n/a	chr4:121844039-121844060 chr4:121843900-121843914 chr4:121843940-121843954
15	POLR2A	chr4:121842715-121844610	HUVEC	blood vessel:	n/a	n/a
16	EP300	chr4:121843731-121844453	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBP	chr4:121842519-121844482	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:121843132-121844493	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3A	chr4:121842523-121844717	H1-hESC	embryonic stem cell:	n/a	chr4:121843390-121843401
20	TCF12	chr4:121843963-121844605	A549	lung:	n/a	n/a
21	POLR2A	chr4:121844060-121844542	H1-neurons	neurons:	n/a	n/a
22	E2F6	chr4:121843772-121844467	A549	lung:	n/a	chr4:121844050-121844059
23	POLR2A	chr4:121843056-121844505	HEK293	kidney:	n/a	n/a
24	POLR2A	chr4:121842827-121844442	IMR90	lung:	n/a	n/a
25	TEAD4	chr4:121843683-121844475	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr4:121842801-121844431	ECC-1	luminal epithelium:	n/a	chr4:121843282-121843291 chr4:121843446-121843456
27	EGR1	chr4:121843711-121844471	H1-hESC	embryonic stem cell:	n/a	n/a
28	E2F6	chr4:121843574-121844548	H1-hESC	embryonic stem cell:	n/a	chr4:121844050-121844059 chr4:121843651-121843661
29	POLR2A	chr4:121842962-121844428	ECC-1	luminal epithelium:	n/a	n/a
30	CHD2	chr4:121843773-121844441	H1-hESC	embryonic stem cell:	n/a	n/a
31	TAF1	chr4:121842695-121844539	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr4:121843120-121844445	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr4:121844280-121844430	NHDF-neo	bronchial:	n/a	n/a
34	CHD1	chr4:121843874-121844514	H1-hESC	embryonic stem cell:	n/a	n/a
35	KAP1	chr4:121843791-121844855	HEK293	kidney:	n/a	n/a
36	GTF2F1	chr4:121843736-121844606	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr4:121842728-121844484	U87	brain:	n/a	n/a
38	TAF7	chr4:121843748-121844473	H1-hESC	embryonic stem cell:	n/a	n/a
39	HA-E2F1	chr4:121842926-121844534	MCF-7	breast:	n/a	chr4:121844084-121844095 chr4:121843445-121843454 chr4:121844050-121844059 chr4:121843651-121843661
40	MAX	chr4:121843663-121844478	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr4:121842691-121844426	A549	lung:	n/a	chr4:121843282-121843291 chr4:121843446-121843456
42	JUND	chr4:121843676-121844485	H1-hESC	embryonic stem cell:	n/a	chr4:121844092-121844106 chr4:121844048-121844057

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:121844401-121844451	PANC-1	pancreas:	n/a
2	chr4:121844401-121844451	MCF10A-Er-Src	breast:	n/a
3	chr4:121844401-121844451	GM12878	blood:	n/a
4	chr4:121844401-121844451	BJ	skin:	n/a
5	chr4:121844401-121844451	RPTEC	kidney:	n/a
6	chr4:121844401-121844451	SAEC	small airway:	n/a
7	chr4:121844401-121844451	Hela-S3	cervix:	n/a
8	chr4:121844401-121844451	CMK	blood:	n/a
9	chr4:121844401-121844451	GM06990	blood:	n/a
10	chr4:121844401-121844451	PFSK-1	brain:	n/a
11	chr4:121844401-121844451	ovcar-3	ovarian:	n/a
12	chr4:121844401-121844451	HRE	kidney:	n/a
13	chr4:121844401-121844451	IMR90	lung:	fetal
14	chr4:121844401-121844451	NH-A	brain:	n/a
15	chr4:121844401-121844451	NT2-D1	testis:	n/a
16	chr4:121844401-121844451	HCM	heart:	n/a
17	chr4:121844401-121844451	BE2_C	brain:	n/a
18	chr4:121844401-121844451	Caco-2	colon:	n/a
19	chr4:121844401-121844451	HCT-116	colon:	n/a
20	chr4:121844401-121844451	AG09309	skin:	n/a
21	chr4:121844401-121844451	NB4	blood:	n/a
22	chr4:121844401-121844451	HIPEpiC	eye:	n/a
23	chr4:121844401-121844451	SK-N-SH_RA	brain:	n/a
24	chr4:121844401-121844451	SK-N-MC	brain:	n/a
25	chr4:121844401-121844451	HepG2	liver:	n/a
26	chr4:121844401-121844451	MCF-7	breast:	n/a
27	chr4:121844401-121844451	HAEpiC	amniotic membrane:	n/a
28	chr4:121844401-121844451	HEK293	kidney:	embryo
29	chr4:121844401-121844451	AG09319	gingival:	n/a
30	chr4:121844401-121844451	A549	lung:	n/a
31	chr4:121844401-121844451	GM12891	blood:	n/a
32	chr4:121844401-121844451	HEEpiC	esophagus:	n/a
33	chr4:121844401-121844451	ProgFib	skin:	n/a
34	chr4:121844401-121844451	H1-hESC	embryonic stem cell:	embryo
35	chr4:121844401-121844451	HMEC	breast:	n/a
36	chr4:121844401-121844451	SK-N-SH	brain:	n/a
37	chr4:121844401-121844451	NHDF-neo	bronchial:	n/a
38	chr4:121844401-121844451	AoSMC	blood vessel:	n/a
39	chr4:121844401-121844451	HL-60	blood:	n/a
40	chr4:121844401-121844451	HRPEpiC	eye:	n/a
41	chr4:121844401-121844451	AG04450	lung:	fetal
42	chr4:121844401-121844451	LNCaP	prostate:	n/a
43	chr4:121844401-121844451	T-47D	breast:	n/a
44	chr4:121844401-121844451	HCPEpiC	choroid plexus:	n/a
45	chr4:121844401-121844451	NHBE	bronchial:	n/a
46	chr4:121844401-121844451	HPAEpiC	pulmonary alveolar:	n/a
47	chr4:121844401-121844451	GM12892	blood:	n/a
48	chr4:121844401-121844451	HUVEC	blood vessel:	n/a
49	chr4:121844401-121844451	PrEC	prostate:	n/a
50	chr4:121844401-121844451	K562	blood:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC079341.1-10	chr4:121843097-121844760	NONHSAT098131

No data

Variant related genes	Relation type
PRDM5	TF binding region
PRDM5	CpG island

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10006503	0.88[ASN][1000 genomes]
rs10857075	0.85[ASN][1000 genomes]
rs10857076	0.88[ASN][1000 genomes]
rs1376109	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1450459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1450472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1450473	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs1450475	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs1450479	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1511314	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs171069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs180730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs180731	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs184668	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs184669	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1901136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2167207	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2198032	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597548	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2667175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2667176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3106313	0.81[CEU][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3114955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3115312	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3115314	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343178	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs343180	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs343195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343198	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343200	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343202	0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs343203	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs343205	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs343212	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs4833187	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs4833694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870252	0.86[CHB][hapmap];0.90[JPT][hapmap]

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	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3405799	chr4:121842552-121845050	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1530799	IL21	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121841800-121844600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr4:121842400-121844600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:121842400-121844600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:121842400-121844800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr4:121842600-121844600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr4:121842600-121844600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:121842600-121844600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:121842600-121844600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:121842600-121844600	Active TSS	Brain Angular Gyrus	brain
10	chr4:121842600-121844600	Active TSS	Brain Anterior Caudate	brain
11	chr4:121842600-121844600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr4:121842600-121844600	Active TSS	Brain Substantia Nigra	brain
13	chr4:121842600-121844600	Active TSS	Fetal Muscle Trunk	muscle
14	chr4:121842600-121844600	Active TSS	Left Ventricle	heart
15	chr4:121842600-121844600	Active TSS	Ovary	ovary
16	chr4:121842600-121844600	Active TSS	Right Atrium	heart
17	chr4:121842600-121844600	Active TSS	NHDF-Ad	bronchial
18	chr4:121842600-121844800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:121842800-121844600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:121842800-121844600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:121842800-121844600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:121842800-121844600	Active TSS	Aorta	Aorta
23	chr4:121842800-121844600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:121842800-121844600	Active TSS	Colonic Mucosa	Colon
25	chr4:121842800-121844600	Active TSS	Fetal Intestine Large	intestine
26	chr4:121842800-121844600	Active TSS	Fetal Intestine Small	intestine
27	chr4:121842800-121844600	Active TSS	Fetal Muscle Leg	muscle
28	chr4:121842800-121844600	Active TSS	Right Ventricle	heart
29	chr4:121842800-121844600	Active TSS	Stomach Smooth Muscle	stomach
30	chr4:121842800-121844800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr4:121842800-121844800	Active TSS	Psoas Muscle	Psoas
32	chr4:121842800-121844800	Active TSS	HSMM	muscle
33	chr4:121842800-121845000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr4:121842800-121845000	Active TSS	NHLF	lung
35	chr4:121843000-121844600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr4:121843000-121844600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:121843000-121844600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:121843000-121844600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr4:121843000-121844600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:121843000-121844600	Active TSS	Brain Hippocampus Middle	brain
41	chr4:121843000-121844600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr4:121843000-121844600	Active TSS	Fetal Lung	lung
43	chr4:121843000-121844600	Active TSS	Fetal Stomach	stomach
44	chr4:121843000-121844600	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr4:121843000-121844600	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr4:121843000-121844600	Active TSS	HSMMtube	muscle
47	chr4:121843000-121844600	Active TSS	NH-A	brain
48	chr4:121843000-121844800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:121843000-121844800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:121843000-121844800	Active TSS	Pancreas	Pancrea

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