Variant report

Variant	rs11575944
Chromosome Location	chr21:40823465-40823466
allele	A/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	EP300	chr21:40823454-40823786	T-47D	breast:	n/a	n/a
2	MYC	chr21:40823464-40824859	K562	blood:	n/a	n/a
3	PML	chr21:40823308-40824838	K562	blood:	n/a	n/a
4	TAF1	chr21:40823355-40823690	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr21:40823241-40825013	K562	blood:	n/a	chr21:40824576-40824585 chr21:40824234-40824248 chr21:40823678-40823687
6	BHLHE40	chr21:40823381-40823617	K562	blood:	n/a	n/a
7	POLR2A	chr21:40823418-40823967	K562	blood:	n/a	n/a
8	UBTF	chr21:40823363-40823771	K562	blood:	n/a	n/a
9	CUX1	chr21:40823403-40823858	K562	blood:	n/a	n/a
10	SRF	chr21:40823447-40823947	H1-hESC	embryonic stem cell:	n/a	chr21:40823699-40823714 chr21:40823699-40823717 chr21:40823700-40823714
11	FOXA1	chr21:40823392-40823730	T-47D	breast:	n/a	chr21:40823510-40823522
12	JUN	chr21:40821978-40825874	K562	blood:	n/a	chr21:40824576-40824585 chr21:40824514-40824527 chr21:40824572-40824585 chr21:40824234-40824248 chr21:40823678-40823687
13	POLR2A	chr21:40823291-40824209	H1-hESC	embryonic stem cell:	n/a	n/a
14	HEY1	chr21:40823408-40824410	K562	blood:	n/a	n/a
15	ZNF384	chr21:40823434-40824179	K562	blood:	n/a	n/a
16	EP300	chr21:40823311-40823847	T-47D	breast:	n/a	n/a
17	ZC3H11A	chr21:40823266-40823876	K562	blood:	n/a	n/a
18	MAZ	chr21:40823228-40825224	K562	blood:	n/a	n/a
19	SRF	chr21:40823239-40824119	MCF-7	breast:	n/a	chr21:40823699-40823714 chr21:40823699-40823717 chr21:40823700-40823714
20	GATA3	chr21:40823421-40823950	T-47D	breast:	n/a	n/a
21	POLR2A	chr21:40823304-40824834	U87	brain:	n/a	n/a
22	RCOR1	chr21:40823391-40825209	K562	blood:	n/a	n/a
23	EP300	chr21:40823345-40825867	K562	blood:	n/a	chr21:40824144-40824158
24	ZMIZ1	chr21:40823429-40825112	K562	blood:	n/a	n/a
25	TEAD4	chr21:40823267-40825247	K562	blood:	n/a	n/a
26	UBTF	chr21:40823408-40824383	K562	blood:	n/a	n/a
27	ZNF143	chr21:40823461-40824030	K562	blood:	n/a	n/a
28	POLR2A	chr21:40823304-40824828	U87	brain:	n/a	n/a
29	TBL1XR1	chr21:40823245-40823984	K562	blood:	n/a	n/a
30	TAF1	chr21:40823457-40823795	K562	blood:	n/a	n/a
31	SRF	chr21:40823409-40824069	MCF-7	breast:	n/a	chr21:40823699-40823714 chr21:40823699-40823717 chr21:40823700-40823714
32	POLR2A	chr21:40823393-40825312	K562	blood:	n/a	n/a
33	SP1	chr21:40823404-40823908	H1-hESC	embryonic stem cell:	n/a	chr21:40823637-40823648
34	FOXA1	chr21:40823075-40823704	T-47D	breast:	n/a	chr21:40823510-40823522 chr21:40823114-40823126
35	MAX	chr21:40823440-40824441	K562	blood:	n/a	n/a
36	MAFK	chr21:40823409-40824692	K562	blood:	n/a	n/a
37	POLR2A	chr21:40823375-40824117	U87	brain:	n/a	n/a
38	MAX	chr21:40823261-40824740	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40800116..40802952-chr21:40820049..40823692,3	K562	blood:
2	chr21:40720444..40722867-chr21:40823306..40826080,2	MCF-7	breast:
3	chr21:40686237..40688163-chr21:40821826..40824303,2	MCF-7	breast:
4	chr21:40800116..40802106-chr21:40821087..40823692,2	K562	blood:
5	chr21:40823323..40825964-chr21:40833634..40835639,2	K562	blood:
6	chr21:40720043..40722488-chr21:40820831..40823616,2	K562	blood:
7	chr21:40554460..40556456-chr21:40823248..40825971,3	K562	blood:
8	chr21:40797216..40799492-chr21:40822971..40825535,2	MCF-7	breast:
9	chr21:40759594..40762847-chr21:40823318..40826677,3	K562	blood:
10	chr21:40759594..40762847-chr21:40822621..40825193,3	K562	blood:

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

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12483547	0.95[ASN][1000 genomes]
rs13050837	0.95[ASN][1000 genomes]
rs13051054	0.95[ASN][1000 genomes]
rs13051142	0.89[ASN][1000 genomes]
rs2049823	0.99[ASN][1000 genomes]
rs2178881	0.80[AMR][1000 genomes]
rs2837014	0.81[ASN][1000 genomes]
rs2837033	0.81[ASN][1000 genomes]
rs2837038	0.86[ASN][1000 genomes]
rs4816626	0.92[ASN][1000 genomes]
rs4816628	0.98[ASN][1000 genomes]
rs7277602	0.98[ASN][1000 genomes]
rs7277633	0.95[ASN][1000 genomes]
rs9979289	0.98[ASN][1000 genomes]
rs9983100	0.92[ASN][1000 genomes]
rs9983180	0.95[ASN][1000 genomes]
rs9983404	0.94[ASN][1000 genomes]
rs9983716	0.95[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11575944	WRB	cis	Thyroid	GTEx
rs11575944	LCA5L	cis	Esophagus Mucosa	GTEx
rs11575944	LCA5L	cis	Thyroid	GTEx
rs11575944	LCA5L	cis	Esophagus Muscularis	GTEx
rs11575944	LCA5L	cis	Muscle Skeletal	GTEx
rs11575944	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40818200-40823600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:40818400-40823600	Weak transcription	Brain Angular Gyrus	brain
3	chr21:40818400-40823600	Weak transcription	Fetal Stomach	stomach
4	chr21:40818400-40823600	Weak transcription	Pancreas	Pancrea
5	chr21:40818600-40823600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr21:40818600-40823600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr21:40818600-40823600	Weak transcription	Brain Hippocampus Middle	brain
8	chr21:40818800-40823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr21:40819000-40823600	Weak transcription	Stomach Mucosa	stomach
10	chr21:40820000-40823600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr21:40820400-40823800	Enhancers	Fetal Heart	heart
12	chr21:40822200-40823800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr21:40822400-40823600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr21:40822400-40823600	Enhancers	Adipose Nuclei	Adipose
15	chr21:40822600-40824600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr21:40822800-40823600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr21:40822800-40823600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr21:40822800-40825200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:40822800-40828600	Active TSS	Right Ventricle	heart
20	chr21:40823000-40823600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr21:40823000-40823600	Weak transcription	Brain Anterior Caudate	brain
22	chr21:40823000-40823600	Weak transcription	Left Ventricle	heart
23	chr21:40823000-40824600	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr21:40823000-40825400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr21:40823000-40825800	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr21:40823200-40823600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr21:40823200-40823600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr21:40823200-40823600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr21:40823200-40823600	Active TSS	Fetal Muscle Trunk	muscle
30	chr21:40823200-40823600	Enhancers	Stomach Smooth Muscle	stomach
31	chr21:40823200-40823600	Enhancers	HSMM	muscle
32	chr21:40823200-40823600	Enhancers	NHEK	skin
33	chr21:40823200-40823800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr21:40823200-40824000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
35	chr21:40823200-40824200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr21:40823200-40824200	Flanking Active TSS	HSMMtube	muscle
37	chr21:40823200-40824400	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr21:40823200-40824400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr21:40823200-40824400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr21:40823200-40824600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr21:40823200-40825200	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr21:40823200-40825400	Active TSS	Psoas Muscle	Psoas
43	chr21:40823200-40825400	Flanking Active TSS	K562	blood
44	chr21:40823200-40825600	Active TSS	Right Atrium	heart
45	chr21:40823400-40823600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr21:40823400-40823600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr21:40823400-40823600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr21:40823400-40823600	Enhancers	HMEC	breast
49	chr21:40823400-40823800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr21:40823400-40823800	Enhancers	HepG2	liver

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