Variant report

Variant	rs11575939
Chromosome Location	chr21:40823902-40823903
allele	C/G
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	MYC	chr21:40823464-40824859	K562	blood:	n/a	n/a
2	HCFC1	chr21:40823474-40824708	K562	blood:	n/a	n/a
3	CTCF	chr21:40823469-40823985	K562	blood:	n/a	n/a
4	PML	chr21:40823308-40824838	K562	blood:	n/a	n/a
5	JUND	chr21:40823241-40825013	K562	blood:	n/a	chr21:40824576-40824585 chr21:40824234-40824248 chr21:40823678-40823687
6	POLR2A	chr21:40823418-40823967	K562	blood:	n/a	n/a
7	ARID3A	chr21:40823574-40824633	K562	blood:	n/a	n/a
8	SRF	chr21:40823447-40823947	H1-hESC	embryonic stem cell:	n/a	chr21:40823699-40823714 chr21:40823699-40823717 chr21:40823700-40823714
9	JUN	chr21:40821978-40825874	K562	blood:	n/a	chr21:40824576-40824585 chr21:40824514-40824527 chr21:40824572-40824585 chr21:40824234-40824248 chr21:40823678-40823687
10	POLR2A	chr21:40823291-40824209	H1-hESC	embryonic stem cell:	n/a	n/a
11	HEY1	chr21:40823408-40824410	K562	blood:	n/a	n/a
12	ZNF384	chr21:40823434-40824179	K562	blood:	n/a	n/a
13	NFYA	chr21:40823545-40823978	K562	blood:	n/a	chr21:40823676-40823691 chr21:40823765-40823780 chr21:40823676-40823691 chr21:40823765-40823780 chr21:40823672-40823690 chr21:40823764-40823776 chr21:40823806-40823818 chr21:40823765-40823779 chr21:40823765-40823778
14	FOS	chr21:40823521-40824004	K562	blood:	n/a	chr21:40823678-40823687
15	TBP	chr21:40823472-40824102	K562	blood:	n/a	n/a
16	IRF1	chr21:40823473-40824185	K562	blood:	n/a	chr21:40824147-40824160 chr21:40824143-40824157 chr21:40824147-40824158 chr21:40824147-40824161 chr21:40824145-40824159 chr21:40824146-40824160
17	TAF1	chr21:40823774-40824049	H1-hESC	embryonic stem cell:	n/a	n/a
18	ELK1	chr21:40823899-40824034	K562	blood:	n/a	n/a
19	MAZ	chr21:40823228-40825224	K562	blood:	n/a	n/a
20	POLR2A	chr21:40823776-40824040	H1-hESC	embryonic stem cell:	n/a	n/a
21	SRF	chr21:40823239-40824119	MCF-7	breast:	n/a	chr21:40823699-40823714 chr21:40823699-40823717 chr21:40823700-40823714
22	HMGN3	chr21:40823635-40824002	K562	blood:	n/a	n/a
23	GATA3	chr21:40823421-40823950	T-47D	breast:	n/a	n/a
24	POLR2A	chr21:40823304-40824834	U87	brain:	n/a	n/a
25	RCOR1	chr21:40823391-40825209	K562	blood:	n/a	n/a
26	EP300	chr21:40823345-40825867	K562	blood:	n/a	chr21:40824144-40824158
27	ZMIZ1	chr21:40823429-40825112	K562	blood:	n/a	n/a
28	CCNT2	chr21:40823593-40824065	K562	blood:	n/a	n/a
29	BHLHE40	chr21:40823857-40824226	K562	blood:	n/a	n/a
30	RCOR1	chr21:40823611-40823972	K562	blood:	n/a	n/a
31	NFYB	chr21:40823478-40824004	K562	blood:	n/a	chr21:40823676-40823691 chr21:40823765-40823780 chr21:40823676-40823691 chr21:40823765-40823780 chr21:40823764-40823776 chr21:40823806-40823818 chr21:40823765-40823779 chr21:40823765-40823778
32	POLR2A	chr21:40823475-40825762	K562	blood:	n/a	n/a
33	TEAD4	chr21:40823267-40825247	K562	blood:	n/a	n/a
34	UBTF	chr21:40823408-40824383	K562	blood:	n/a	n/a
35	ATF1	chr21:40823550-40824822	K562	blood:	n/a	n/a
36	ZNF143	chr21:40823461-40824030	K562	blood:	n/a	n/a
37	SP1	chr21:40823494-40823924	H1-hESC	embryonic stem cell:	n/a	chr21:40823637-40823648
38	POLR2A	chr21:40823304-40824828	U87	brain:	n/a	n/a
39	TBL1XR1	chr21:40823245-40823984	K562	blood:	n/a	n/a
40	CHD2	chr21:40823565-40823936	K562	blood:	n/a	n/a
41	SRF	chr21:40823409-40824069	MCF-7	breast:	n/a	chr21:40823699-40823714 chr21:40823699-40823717 chr21:40823700-40823714
42	POLR2A	chr21:40823393-40825312	K562	blood:	n/a	n/a
43	SP1	chr21:40823404-40823908	H1-hESC	embryonic stem cell:	n/a	chr21:40823637-40823648
44	MAX	chr21:40823440-40824441	K562	blood:	n/a	n/a
45	MAFK	chr21:40823409-40824692	K562	blood:	n/a	n/a
46	POLR2A	chr21:40823375-40824117	U87	brain:	n/a	n/a
47	MAX	chr21:40823261-40824740	K562	blood:	n/a	n/a
48	TBP	chr21:40823479-40824013	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40720444..40722867-chr21:40823306..40826080,2	MCF-7	breast:
2	chr21:40686237..40688163-chr21:40821826..40824303,2	MCF-7	breast:
3	chr21:40823323..40825964-chr21:40833634..40835639,2	K562	blood:
4	chr21:40554460..40556456-chr21:40823248..40825971,3	K562	blood:
5	chr21:40797216..40799492-chr21:40822971..40825535,2	MCF-7	breast:
6	chr21:40759594..40762847-chr21:40823318..40826677,3	K562	blood:
7	chr21:40759594..40762847-chr21:40822621..40825193,3	K562	blood:
8	chr21:40554955..40557163-chr21:40823681..40826162,2	K562	blood:

Variant related genes	Relation type
SH3BGR	TF binding region
ENSG00000183527	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000272991	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs16997618	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065313	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205200	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205201	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223028	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246078	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410128	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837009	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837015	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837017	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837018	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837019	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837020	0.93[ASN][1000 genomes]
rs2837021	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837022	1.00[ASN][1000 genomes]
rs2837023	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837024	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837025	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837026	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837029	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837030	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837031	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837032	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837034	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837037	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837039	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837040	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840267	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281987	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56812456	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56866897	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58900137	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596289	0.80[ASN][1000 genomes]
rs61342945	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275686	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276575	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276981	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277627	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279753	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73365952	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73367928	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367958	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367962	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367974	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367976	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906032	0.81[ASN][1000 genomes]
rs73906033	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73906034	0.81[ASN][1000 genomes]
rs940625	0.80[ASN][1000 genomes]
rs9680443	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11575939	WRB	cis	Adipose Subcutaneous	GTEx
rs11575939	SH3BGR	cis	Artery Tibial	GTEx
rs11575939	SH3BGR	cis	Adipose Subcutaneous	GTEx
rs11575939	LCA5L	cis	Nerve Tibial	GTEx
rs11575939	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs11575939	WRB	cis	lung	GTEx
rs11575939	LCA5L	cis	Artery Tibial	GTEx
rs11575939	LCA5L	cis	Thyroid	GTEx
rs11575939	WRB	cis	Artery Tibial	GTEx
rs11575939	WRB	cis	Nerve Tibial	GTEx
rs11575939	LCA5L	cis	Esophagus Muscularis	GTEx
rs11575939	LCA5L	cis	lung	GTEx
rs11575939	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40822600-40824600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr21:40822800-40825200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:40822800-40828600	Active TSS	Right Ventricle	heart
4	chr21:40823000-40824600	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr21:40823000-40825400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr21:40823000-40825800	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr21:40823200-40824000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
8	chr21:40823200-40824200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr21:40823200-40824200	Flanking Active TSS	HSMMtube	muscle
10	chr21:40823200-40824400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr21:40823200-40824400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr21:40823200-40824400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr21:40823200-40824600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr21:40823200-40825200	Flanking Active TSS	Fetal Muscle Leg	muscle
15	chr21:40823200-40825400	Active TSS	Psoas Muscle	Psoas
16	chr21:40823200-40825400	Flanking Active TSS	K562	blood
17	chr21:40823200-40825600	Active TSS	Right Atrium	heart
18	chr21:40823400-40824000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr21:40823400-40824000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr21:40823400-40824400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr21:40823400-40824400	Enhancers	Fetal Lung	lung
22	chr21:40823400-40824800	Enhancers	Fetal Brain Male	brain
23	chr21:40823400-40825000	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr21:40823400-40825200	Active TSS	Brain Cingulate Gyrus	brain
25	chr21:40823400-40825200	Active TSS	Rectal Smooth Muscle	rectum
26	chr21:40823400-40825400	Active TSS	Aorta	Aorta
27	chr21:40823400-40825800	Active TSS	Brain Substantia Nigra	brain
28	chr21:40823600-40824000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr21:40823600-40824000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr21:40823600-40824000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr21:40823600-40824000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr21:40823600-40824000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr21:40823600-40824000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr21:40823600-40824000	Flanking Active TSS	Fetal Muscle Trunk	muscle
35	chr21:40823600-40824000	Active TSS	Pancreas	Pancrea
36	chr21:40823600-40824000	Flanking Active TSS	HMEC	breast
37	chr21:40823600-40824000	Bivalent/Poised TSS	Osteobl	bone
38	chr21:40823600-40824200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr21:40823600-40824200	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr21:40823600-40824200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr21:40823600-40824200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr21:40823600-40824200	Enhancers	Stomach Mucosa	stomach
43	chr21:40823600-40824200	Flanking Active TSS	NHEK	skin
44	chr21:40823600-40824400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr21:40823600-40824400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr21:40823600-40824400	Active TSS	Fetal Brain Female	brain
47	chr21:40823600-40824400	Flanking Active TSS	HSMM	muscle
48	chr21:40823600-40824600	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr21:40823600-40824800	Active TSS	H9 Cell Line	embryonic stem cell
50	chr21:40823600-40825000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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