Variant report

Variant	rs4816628
Chromosome Location	chr21:40822940-40822941
allele	A/C
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	JUN	chr21:40821978-40825874	K562	blood:	n/a	chr21:40824576-40824585 chr21:40824514-40824527 chr21:40824572-40824585 chr21:40824234-40824248 chr21:40823678-40823687

No.	Distal block	Cell Line	Cell type
1	chr21:40800116..40802952-chr21:40820049..40823692,3	K562	blood:
2	chr21:40686237..40688163-chr21:40821826..40824303,2	MCF-7	breast:
3	chr21:40800116..40802106-chr21:40821087..40823692,2	K562	blood:
4	chr21:40720043..40722488-chr21:40820831..40823616,2	K562	blood:
5	chr21:40759594..40762847-chr21:40822621..40825193,3	K562	blood:

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

Extended variants
information (count: 29 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11575944	0.98[ASN][1000 genomes]
rs12483547	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13050837	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13051054	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13051142	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2009713	0.82[TSI][hapmap]
rs2049823	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837010	0.86[JPT][hapmap]
rs2837011	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2837012	0.86[JPT][hapmap]
rs2837013	0.86[JPT][hapmap]
rs2837014	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2837016	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2837027	0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs2837033	0.80[ASN][1000 genomes]
rs2837038	0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4816626	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7277602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7277633	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8130381	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs9979289	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979353	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9983100	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9983180	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9983404	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9983435	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs9983716	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs4816628	WRB	cis	Artery Tibial	GTEx
rs4816628	LCA5L	cis	Muscle Skeletal	GTEx
rs4816628	LCA5L	cis	lung	GTEx
rs4816628	LCA5L	cis	Esophagus Muscularis	GTEx
rs4816628	LCA5L	cis	Esophagus Mucosa	GTEx
rs4816628	SH3BGR	cis	Thyroid	GTEx
rs4816628	WRB	cis	Thyroid	GTEx
rs4816628	WRB	cis	parietal	SCAN
rs4816628	C21orf121	cis	cerebellum	SCAN
rs4816628	WRB	cis	lung	GTEx
rs4816628	LCA5L	cis	Nerve Tibial	GTEx
rs4816628	LCA5L	cis	Stomach	GTEx
rs4816628	WRB	cis	cerebellum	SCAN
rs4816628	LCA5L	cis	Adipose Subcutaneous	GTEx
rs4816628	LCA5L	cis	parietal	SCAN
rs4816628	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs4816628	LCA5L	cis	Artery Tibial	GTEx
rs4816628	LCA5L	cis	Thyroid	GTEx
rs4816628	LCA5L	cis	Artery Aorta	GTEx
rs4816628	HMGN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40818200-40823200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr21:40818200-40823200	Weak transcription	HSMM	muscle
3	chr21:40818200-40823400	Weak transcription	Aorta	Aorta
4	chr21:40818200-40823600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:40818400-40823200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr21:40818400-40823200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr21:40818400-40823200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr21:40818400-40823400	Weak transcription	Fetal Lung	lung
9	chr21:40818400-40823600	Weak transcription	Brain Angular Gyrus	brain
10	chr21:40818400-40823600	Weak transcription	Fetal Stomach	stomach
11	chr21:40818400-40823600	Weak transcription	Pancreas	Pancrea
12	chr21:40818600-40823200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr21:40818600-40823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr21:40818600-40823200	Weak transcription	HSMMtube	muscle
15	chr21:40818600-40823400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr21:40818600-40823400	Weak transcription	HMEC	breast
17	chr21:40818600-40823600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr21:40818600-40823600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr21:40818600-40823600	Weak transcription	Brain Hippocampus Middle	brain
20	chr21:40818800-40823200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr21:40818800-40823200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr21:40818800-40823400	Weak transcription	Fetal Brain Male	brain
23	chr21:40818800-40823400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr21:40818800-40823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr21:40819000-40823600	Weak transcription	Stomach Mucosa	stomach
26	chr21:40819200-40823400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr21:40820000-40823000	Weak transcription	Fetal Muscle Leg	muscle
28	chr21:40820000-40823600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr21:40820400-40823800	Enhancers	Fetal Heart	heart
30	chr21:40821000-40823200	Enhancers	K562	blood
31	chr21:40821200-40823400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr21:40821600-40823000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr21:40821800-40823200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr21:40822200-40823000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr21:40822200-40823000	Enhancers	Left Ventricle	heart
36	chr21:40822200-40823800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr21:40822400-40823200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr21:40822400-40823200	Enhancers	Psoas Muscle	Psoas
39	chr21:40822400-40823400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr21:40822400-40823600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr21:40822400-40823600	Enhancers	Adipose Nuclei	Adipose
42	chr21:40822600-40823000	Enhancers	Brain Anterior Caudate	brain
43	chr21:40822600-40823400	Enhancers	Brain Substantia Nigra	brain
44	chr21:40822600-40824600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr21:40822800-40823000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr21:40822800-40823000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr21:40822800-40823200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr21:40822800-40823600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr21:40822800-40823600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr21:40822800-40825200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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