Variant report

Variant	rs2239384
Chromosome Location	chr21:40722070-40722071
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:72)
CpG islands
(count:61)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:72 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40721258-40722114	HL-60	blood:	n/a	n/a
2	MTA3	chr21:40721256-40722732	GM12878	blood:	n/a	n/a
3	POLR2A	chr21:40720321-40722997	K562	blood:	n/a	n/a
4	TBL1XR1	chr21:40721287-40722811	K562	blood:	n/a	n/a
5	MAZ	chr21:40720171-40722416	GM12878	blood:	n/a	n/a
6	TAF1	chr21:40721191-40722259	MCF-7	breast:	n/a	n/a
7	POLR2A	chr21:40720101-40723328	K562	blood:	n/a	n/a
8	POLR2A	chr21:40719451-40723014	GM12878	blood:	n/a	n/a
9	POLR2A	chr21:40716164-40723345	K562	blood:	n/a	n/a
10	TEAD4	chr21:40721177-40722666	K562	blood:	n/a	chr21:40722106-40722115
11	ELF1	chr21:40721132-40722351	MCF-7	breast:	n/a	chr21:40721489-40721502
12	SIN3AK20	chr21:40719291-40722472	MCF-7	breast:	n/a	n/a
13	EBF1	chr21:40722033-40722340	GM12878	blood:	n/a	n/a
14	MAX	chr21:40721154-40722801	MCF-7	breast:	n/a	n/a
15	POLR2A	chr21:40721197-40722106	SK-N-MC	brain:	n/a	n/a
16	PML	chr21:40721175-40722098	GM12878	blood:	n/a	n/a
17	POLR2A	chr21:40721208-40722087	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr21:40720291-40722386	NB4	blood:	n/a	n/a
19	MAX	chr21:40721114-40722093	HepG2	liver:	n/a	n/a
20	YY1	chr21:40721537-40722072	GM12892	blood:	n/a	n/a
21	ZNF384	chr21:40721364-40722387	K562	blood:	n/a	n/a
22	MYC	chr21:40719529-40722622	K562	blood:	n/a	n/a
23	POLR2A	chr21:40720095-40722140	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr21:40720156-40722146	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr21:40721209-40722088	K562	blood:	n/a	n/a
26	PML	chr21:40721160-40722107	MCF-7	breast:	n/a	n/a
27	POLR2A	chr21:40720187-40723493	K562	blood:	n/a	n/a
28	MAX	chr21:40721189-40722072	K562	blood:	n/a	n/a
29	POLR2A	chr21:40721192-40722077	GM12892	blood:	n/a	n/a
30	MAX	chr21:40721151-40722160	A549	lung:	n/a	n/a
31	MAX	chr21:40720257-40722086	GM12878	blood:	n/a	n/a
32	MYBL2	chr21:40721210-40722125	HepG2	liver:	n/a	n/a
33	POLR2A	chr21:40719412-40723072	GM12891	blood:	n/a	n/a
34	JUND	chr21:40720384-40722664	K562	blood:	n/a	chr21:40721637-40721646 chr21:40721326-40721335
35	POLR2A	chr21:40720270-40723072	Raji	blood:	n/a	n/a
36	POLR2A	chr21:40720182-40722538	GM12892	blood:	n/a	n/a
37	POLR2A	chr21:40720143-40722611	GM19193	blood:	n/a	n/a
38	EGR1	chr21:40720856-40722111	MCF-7	breast:	n/a	chr21:40721601-40721615 chr21:40721584-40721593
39	POLR2A	chr21:40721214-40722071	GM12878	blood:	n/a	n/a
40	HEY1	chr21:40721233-40722087	K562	blood:	n/a	n/a
41	POLR2A	chr21:40719490-40723323	GM12878	blood:	n/a	n/a
42	POLR2A	chr21:40720193-40722206	GM19099	blood:	n/a	n/a
43	POLR2A	chr21:40721224-40722135	GM12892	blood:	n/a	n/a
44	POLR2A	chr21:40721178-40722080	GM12892	blood:	n/a	n/a
45	POLR2A	chr21:40721242-40722165	HepG2	liver:	n/a	n/a
46	MAX	chr21:40721203-40722073	MCF-7	breast:	n/a	n/a
47	RCOR1	chr21:40721351-40722488	K562	blood:	n/a	n/a
48	MXI1	chr21:40721205-40722958	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr21:40720192-40723374	K562	blood:	n/a	n/a
50	POLR2A	chr21:40721179-40723096	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:40722023-40722073	RPTEC	kidney:	n/a
2	chr21:40722023-40722073	HRE	kidney:	n/a
3	chr21:40722023-40722073	NT2-D1	testis:	n/a
4	chr21:40722023-40722073	H1-hESC	embryonic stem cell:	embryo
5	chr21:40722023-40722073	GM12892	blood:	n/a
6	chr21:40722023-40722073	HL-60	blood:	n/a
7	chr21:40722023-40722073	AoSMC	blood vessel:	n/a
8	chr21:40722023-40722073	AG04450	lung:	fetal
9	chr21:40722023-40722073	AG09319	gingival:	n/a
10	chr21:40722023-40722073	HRCEpiC	kidney:	n/a
11	chr21:40722023-40722073	SAEC	small airway:	n/a
12	chr21:40722023-40722073	AG10803	skin:	n/a
13	chr21:40722023-40722073	HRPEpiC	eye:	n/a
14	chr21:40722023-40722073	HNPCEpiC	eye:	n/a
15	chr21:40722023-40722073	A549	lung:	n/a
16	chr21:40722023-40722073	HEK293	kidney:	embryo
17	chr21:40722023-40722073	PFSK-1	brain:	n/a
18	chr21:40722023-40722073	SK-N-SH	brain:	n/a
19	chr21:40722023-40722073	K562	blood:	n/a
20	chr21:40722023-40722073	PrEC	prostate:	n/a
21	chr21:40722023-40722073	HCT-116	colon:	n/a
22	chr21:40722023-40722073	HUVEC	blood vessel:	n/a
23	chr21:40722023-40722073	HepG2	liver:	n/a
24	chr21:40722023-40722073	Jurkat	blood:	n/a
25	chr21:40722023-40722073	HIPEpiC	eye:	n/a
26	chr21:40722023-40722073	HCM	heart:	n/a
27	chr21:40722023-40722073	GM12878	blood:	n/a
28	chr21:40722023-40722073	CMK	blood:	n/a
29	chr21:40722023-40722073	GM06990	blood:	n/a
30	chr21:40722023-40722073	NHBE	bronchial:	n/a
31	chr21:40722023-40722073	ovcar-3	ovarian:	n/a
32	chr21:40722023-40722073	HPAEpiC	pulmonary alveolar:	n/a
33	chr21:40722023-40722073	SKMC	muscle:	n/a
34	chr21:40722023-40722073	BE2_C	brain:	n/a
35	chr21:40722023-40722073	PANC-1	pancreas:	n/a
36	chr21:40722023-40722073	NH-A	brain:	n/a
37	chr21:40722023-40722073	Hela-S3	cervix:	n/a
38	chr21:40722023-40722073	U87	brain:	n/a
39	chr21:40722023-40722073	ECC-1	luminal epithelium:	n/a
40	chr21:40722023-40722073	T-47D	breast:	n/a
41	chr21:40722023-40722073	ProgFib	skin:	n/a
42	chr21:40722023-40722073	HCPEpiC	choroid plexus:	n/a
43	chr21:40722023-40722073	HMEC	breast:	n/a
44	chr21:40722023-40722073	HAEpiC	amniotic membrane:	n/a
45	chr21:40722023-40722073	SK-N-MC	brain:	n/a
46	chr21:40722023-40722073	BJ	skin:	n/a
47	chr21:40722023-40722073	HCF	heart:	n/a
48	chr21:40722023-40722073	Caco-2	colon:	n/a
49	chr21:40722023-40722073	GM12891	blood:	n/a
50	chr21:40722023-40722073	IMR90	lung:	fetal

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40635630..40638349-chr21:40720638..40723544,2	MCF-7	breast:
2	chr11:14541657..14542383-chr21:40721262..40722122,2	NB4	blood:
3	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
4	chr21:40550592..40552295-chr21:40721972..40724130,2	K562	blood:
5	chr21:40650772..40652472-chr21:40721952..40724679,2	K562	blood:
6	chr21:40720623..40723017-chr21:40815562..40818761,4	K562	blood:
7	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
8	chr21:40716662..40723444-chr21:40748337..40754328,16	MCF-7	breast:
9	chr21:40719359..40724848-chr21:40748806..40754741,7	MCF-7	breast:
10	chr21:40720444..40722867-chr21:40823306..40826080,2	MCF-7	breast:
11	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
12	chr21:40721779..40723568-chr21:40810701..40813342,2	MCF-7	breast:
13	chr21:40719979..40722729-chr21:40816056..40819504,5	MCF-7	breast:
14	chr21:40719750..40724652-chr21:40748317..40754270,9	K562	blood:
15	chr21:40651445..40653004-chr21:40721446..40723113,2	MCF-7	breast:
16	chr21:40721702..40724513-chr21:40734759..40737368,2	K562	blood:
17	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
18	chr21:40553821..40557385-chr21:40719764..40724370,6	K562	blood:
19	chr21:40719238..40723494-chr21:40813785..40819496,7	MCF-7	breast:
20	chr21:40716961..40722807-chr21:40750720..40754894,10	K562	blood:
21	chr21:40719170..40722188-chr21:40780437..40783108,3	MCF-7	breast:
22	chr21:40719410..40723060-chr21:40814028..40819084,9	K562	blood:
23	chr21:40554663..40558370-chr21:40719503..40722190,4	MCF-7	breast:
24	chr16:85043892..85046309-chr21:40720857..40722668,2	MCF-7	breast:
25	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:

No data

Variant related genes	Relation type
HMGN1	TF binding region
ENSG00000238556	TF binding region
ENSG00000238556	CpG island
HMGN1	CpG island
ENSG00000182093	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000153786	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000256206	Chromatin interaction
ENSG00000129084	Chromatin interaction
ENSG00000227406	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11911475	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12106311	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13433458	0.84[ASN][1000 genomes]
rs1554933	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs1554934	0.87[ASN][1000 genomes]
rs2735313	0.83[ASN][1000 genomes]
rs2776311	0.83[JPT][hapmap]
rs2836990	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs2836992	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2854727	0.83[JPT][hapmap]
rs28629334	0.84[ASN][1000 genomes]
rs3761372	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs4818027	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59805871	0.85[ASN][1000 genomes]
rs6517522	0.83[JPT][hapmap]
rs7279434	0.84[ASN][1000 genomes]
rs741795	0.83[JPT][hapmap]
rs9974653	0.87[ASN][1000 genomes]
rs9983270	0.80[ASN][1000 genomes]
rs9983368	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9983594	0.80[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	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv3439352	chr21:40719607-40722455	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2239384	SH3BGR	cis	Artery Tibial	GTEx
rs2239384	WRB	cis	Adipose Subcutaneous	GTEx
rs2239384	WRB	cis	Thyroid	GTEx
rs2239384	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2239384	HMGN1	cis	multi-tissue	Pritchard
rs2239384	WRB	cis	Artery Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40718800-40722200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr21:40718800-40722200	Active TSS	GM12878-XiMat	blood
3	chr21:40719000-40722200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr21:40719000-40722400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr21:40719200-40722200	Active TSS	Fetal Kidney	kidney
6	chr21:40719200-40722400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr21:40719200-40722800	Active TSS	Hela-S3	cervix
8	chr21:40719400-40722200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr21:40719400-40722200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr21:40719400-40722400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr21:40719400-40722600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr21:40719600-40722200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr21:40719600-40722200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr21:40719600-40722200	Bivalent/Poised TSS	HepG2	liver
15	chr21:40719600-40722400	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr21:40719800-40722200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr21:40719800-40722200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr21:40719800-40722200	Active TSS	Brain Hippocampus Middle	brain
19	chr21:40719800-40722200	Active TSS	Osteobl	bone
20	chr21:40719800-40722400	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr21:40720000-40722200	Active TSS	Brain Cingulate Gyrus	brain
22	chr21:40720000-40722400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr21:40720000-40722400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr21:40720000-40722400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr21:40720000-40722400	Active TSS	Brain Substantia Nigra	brain
26	chr21:40720000-40722600	Active TSS	Rectal Smooth Muscle	rectum
27	chr21:40720200-40722200	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr21:40720200-40722400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr21:40720400-40722400	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr21:40720400-40722400	Active TSS	K562	blood
31	chr21:40720400-40722600	Active TSS	A549	lung
32	chr21:40720600-40722200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:40721000-40722400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr21:40721200-40722200	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr21:40721400-40722200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr21:40721400-40722200	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr21:40721400-40722200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr21:40721400-40722200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr21:40721400-40722400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr21:40721400-40722400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr21:40721600-40722200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr21:40721600-40722200	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr21:40721600-40722200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr21:40721600-40722200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr21:40721600-40722200	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr21:40721600-40722200	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr21:40721600-40722200	Flanking Active TSS	Placenta	Placenta
48	chr21:40721600-40722200	Flanking Active TSS	Fetal Stomach	stomach
49	chr21:40721600-40722400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr21:40721600-40722400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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