Variant report

Variant	rs2244352
Chromosome Location	chr21:40757973-40757974
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr21:40757430-40758329	SK-N-SH	brain:	n/a	chr21:40757946-40757957 chr21:40757946-40757955 chr21:40757943-40757957 chr21:40757946-40757960
2	MYBL2	chr21:40757326-40758187	HepG2	liver:	n/a	n/a
3	POLR2A	chr21:40757705-40758225	MCF-7	breast:	n/a	n/a
4	MAX	chr21:40757342-40758300	A549	lung:	n/a	n/a
5	POLR2A	chr21:40757699-40758337	U87	brain:	n/a	n/a
6	TAF1	chr21:40757630-40758191	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr21:40756239-40759236	HepG2	liver:	n/a	n/a
8	ATF3	chr21:40757394-40758068	HepG2	liver:	n/a	n/a
9	POLR2A	chr21:40757566-40758505	ECC-1	luminal epithelium:	n/a	n/a
10	HNF4G	chr21:40757442-40757984	HepG2	liver:	n/a	chr21:40757694-40757709
11	POLR2A	chr21:40757846-40758130	U87	brain:	n/a	n/a
12	MYC	chr21:40757350-40758100	HepG2	liver:	n/a	n/a
13	MXI1	chr21:40757135-40758592	HepG2	liver:	n/a	n/a
14	SP1	chr21:40757508-40758020	A549	lung:	n/a	n/a
15	POLR2A	chr21:40757773-40758139	PANC-1	pancreas:	n/a	n/a
16	RFX5	chr21:40757096-40758101	HepG2	liver:	n/a	n/a
17	POLR2A	chr21:40756685-40758650	HepG2	liver:	n/a	n/a
18	NRF1	chr21:40757536-40758469	HepG2	liver:	n/a	chr21:40758336-40758347 chr21:40757946-40757957 chr21:40758336-40758345 chr21:40757946-40757955 chr21:40758333-40758347 chr21:40757943-40757957 chr21:40757946-40757960 chr21:40758345-40758354
19	MAX	chr21:40757484-40758211	SK-N-SH	brain:	n/a	n/a
20	CREB1	chr21:40757588-40758091	A549	lung:	n/a	n/a
21	CEBPB	chr21:40757808-40758131	HepG2	liver:	n/a	n/a
22	HNF4A	chr21:40757341-40758033	HepG2	liver:	n/a	chr21:40757750-40757765 chr21:40757695-40757710
23	POLR2A	chr21:40756621-40758606	HepG2	liver:	n/a	n/a
24	POLR2A	chr21:40757089-40758606	HepG2	liver:	n/a	n/a
25	POLR2A	chr21:40757753-40758316	GM12878	blood:	n/a	n/a
26	HEY1	chr21:40756667-40758658	HepG2	liver:	n/a	n/a
27	TAF1	chr21:40757784-40758223	A549	lung:	n/a	n/a
28	TBP	chr21:40757262-40758565	HepG2	liver:	n/a	n/a
29	MAZ	chr21:40757811-40758190	GM12878	blood:	n/a	n/a
30	POLR2A	chr21:40757598-40758077	MCF-7	breast:	n/a	n/a
31	TAF1	chr21:40757202-40758054	HepG2	liver:	n/a	n/a
32	POLR2A	chr21:40757513-40758203	A549	lung:	n/a	n/a
33	RCOR1	chr21:40757287-40758543	HepG2	liver:	n/a	n/a
34	EP300	chr21:40757366-40758012	HepG2	liver:	n/a	n/a
35	MAX	chr21:40757421-40758246	A549	lung:	n/a	n/a
36	POLR2A	chr21:40756585-40758739	HepG2	liver:	n/a	n/a
37	EP300	chr21:40757343-40758131	HepG2	liver:	n/a	n/a
38	MAX	chr21:40757401-40758591	HepG2	liver:	n/a	n/a
39	JUND	chr21:40757537-40758385	HepG2	liver:	n/a	chr21:40758311-40758319
40	POLR2A	chr21:40757495-40758109	A549	lung:	n/a	n/a
41	POLR2A	chr21:40757852-40758052	MCF10A-Er-Src	breast:	n/a	n/a
42	CHD2	chr21:40757606-40758007	GM12878	blood:	n/a	n/a
43	POLR2A	chr21:40757631-40758607	NB4	blood:	n/a	n/a
44	BHLHE40	chr21:40757544-40758086	GM12878	blood:	n/a	n/a
45	USF2	chr21:40757330-40758076	HepG2	liver:	n/a	n/a
46	POLR2A	chr21:40757571-40758473	GM18951	blood:	n/a	n/a
47	MAZ	chr21:40757083-40758474	HepG2	liver:	n/a	n/a
48	ZNF143	chr21:40757852-40758045	GM12878	blood:	n/a	n/a
49	POLR2A	chr21:40757641-40758142	HUVEC	blood vessel:	n/a	n/a
50	MXI1	chr21:40757797-40758021	GM12878	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40757591..40761225-chr21:40763023..40767191,7	K562	blood:
2	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:
3	chr21:40750855..40754449-chr21:40757264..40761324,13	K562	blood:
4	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
5	chr21:40750751..40754678-chr21:40755594..40761324,12	K562	blood:
6	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
7	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
8	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:
9	21:40687235-40690033..21:40757151-40764378	K562	blood:
10	chr21:40750392..40754801-chr21:40757428..40762186,12	MCF-7	breast:
11	chr21:40755802..40758273-chr21:40758369..40760779,2	MCF-7	breast:
12	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
13	chr21:40693407..40696384-chr21:40756189..40758708,3	MCF-7	breast:
14	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
15	21:40686083-40686932..21:40757151-40764378	K562	blood:
16	chr21:40757952..40760815-chr21:40812863..40817486,4	MCF-7	breast:
17	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
18	chr21:40750891..40755008-chr21:40755976..40761346,13	MCF-7	breast:

No data

Variant related genes	Relation type
WRB	TF binding region
ENSG00000252915	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000238141	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1060180	0.81[ASN][1000 genomes]
rs10775662	0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs13051949	0.81[ASN][1000 genomes]
rs13230	0.81[ASN][1000 genomes]
rs1554933	0.85[YRI][hapmap]
rs2299739	0.96[ASN][1000 genomes]
rs2299741	0.81[ASN][1000 genomes]
rs2836990	0.80[YRI][hapmap]
rs2836996	0.89[YRI][hapmap]
rs2836998	0.81[ASN][1000 genomes]
rs2836999	0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs2837000	0.81[ASN][1000 genomes]
rs2837001	0.81[ASN][1000 genomes]
rs2837002	0.81[ASN][1000 genomes]
rs2837003	1.00[ASW][hapmap];0.80[LWK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs2837004	1.00[ASW][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs2837005	0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs2837006	0.80[CHD][hapmap]
rs2837007	0.80[CHD][hapmap]
rs3761372	0.85[YRI][hapmap]
rs3787923	0.81[ASN][1000 genomes]
rs3787924	0.81[ASN][1000 genomes]
rs6517547	0.84[ASN][1000 genomes]
rs8131718	0.81[ASN][1000 genomes]
rs9305674	0.81[ASN][1000 genomes]
rs9974828	0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	nsv1056452	chr21:40741893-40782587	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1063521	chr21:40747754-40790197	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2244352	LCA5L	cis	Nerve Tibial	GTEx
rs2244352	LCA5L	cis	Thyroid	GTEx
rs2244352	WRB	cis	Esophagus Muscularis	GTEx
rs2244352	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2244352	WRB	cis	lung	GTEx
rs2244352	LCA5L	cis	Artery Tibial	GTEx
rs2244352	WRB	cis	Artery Tibial	GTEx
rs2244352	KCNE2	cis	parietal	SCAN
rs2244352	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2244352	HMGN1	cis	lymphoblastoid	seeQTL
rs2244352	WRB	cis	Artery Aorta	GTEx
rs2244352	LCA5L	cis	Stomach	GTEx
rs2244352	HMGN1	cis	multi-tissue	Pritchard
rs2244352	LOC643790	trans	multi-tissue	Pritchard
rs2244352	WRB	cis	multi-tissue	Pritchard
rs2244352	LCA5L	cis	brain	BrainEAC
rs2244352	WRB	cis	parietal	SCAN
rs2244352	WRB	cis	Nerve Tibial	GTEx
rs2244352	WRB	cis	Adipose Subcutaneous	GTEx
rs2244352	LCA5L	cis	lung	GTEx
rs2244352	LCA5L	cis	Esophagus Muscularis	GTEx
rs2244352	WRB	cis	Thyroid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40753000-40758000	Weak transcription	Small Intestine	intestine
2	chr21:40753200-40759400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr21:40753200-40759800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:40753400-40759400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr21:40753400-40759400	Weak transcription	Aorta	Aorta
6	chr21:40753400-40760200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr21:40753600-40758000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr21:40753600-40758000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr21:40753600-40758000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr21:40753600-40758200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr21:40753600-40758400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr21:40753600-40759000	Weak transcription	Hela-S3	cervix
13	chr21:40753600-40759000	Weak transcription	K562	blood
14	chr21:40753600-40759200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr21:40753600-40759200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr21:40753600-40759600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:40754600-40758200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr21:40754800-40759400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr21:40756000-40758000	Active TSS	HepG2	liver
20	chr21:40756200-40758000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr21:40756600-40758000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr21:40756600-40758000	Active TSS	Liver	Liver
23	chr21:40756600-40759200	Enhancers	Fetal Heart	heart
24	chr21:40756600-40759400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr21:40756600-40759600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr21:40756800-40758200	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr21:40757000-40758400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr21:40757000-40758400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
29	chr21:40757000-40758400	Enhancers	Stomach Mucosa	stomach
30	chr21:40757000-40758600	Enhancers	Fetal Brain Male	brain
31	chr21:40757200-40758000	Genic enhancers	Gastric	stomach
32	chr21:40757200-40758400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr21:40757200-40758400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr21:40757200-40758600	Active TSS	Brain Substantia Nigra	brain
35	chr21:40757200-40758600	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr21:40757200-40758600	Flanking Active TSS	Osteobl	bone
37	chr21:40757400-40758000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr21:40757400-40758000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
39	chr21:40757400-40758000	Enhancers	Primary B cells from cord blood	blood
40	chr21:40757400-40758000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr21:40757400-40758000	Active TSS	Duodenum Mucosa	Duodenum
42	chr21:40757400-40758000	Active TSS	Fetal Intestine Large	intestine
43	chr21:40757400-40758000	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr21:40757400-40758200	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr21:40757400-40758200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr21:40757400-40758200	Active TSS	Fetal Kidney	kidney
47	chr21:40757400-40758200	Active TSS	Psoas Muscle	Psoas
48	chr21:40757400-40758200	Active TSS	Rectal Smooth Muscle	rectum
49	chr21:40757400-40758200	Active TSS	GM12878-XiMat	blood
50	chr21:40757400-40758400	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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