Variant report

Variant	rs2837016
Chromosome Location	chr21:40787816-40787817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40758859..40762254-chr21:40785710..40788224,3	MCF-7	breast:
2	chr21:40784167..40788125-chr21:40789270..40793629,5	K562	blood:
3	chr21:40781064..40783289-chr21:40787779..40789319,2	K562	blood:
4	chr21:40786710..40789568-chr21:40816730..40818254,2	K562	blood:

Variant related genes	Relation type
ENSG00000185437	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11088475	0.88[ASN][1000 genomes]
rs2049823	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs2837010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837011	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837012	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837014	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2837027	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2837028	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2837033	0.83[ASN][1000 genomes]
rs2837038	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4816628	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs7276842	0.82[ASN][1000 genomes]
rs7277602	0.86[JPT][hapmap]
rs8129564	0.84[ASN][1000 genomes]
rs8130381	0.94[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9979289	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs9979353	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9983180	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs9983435	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]

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	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	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
3	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
4	esv3430213	chr21:40787789-40788109	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2837016	LCA5L	cis	parietal	SCAN
rs2837016	BRWD1	cis	parietal	SCAN
rs2837016	BRWD1	cis	cerebellum	SCAN
rs2837016	LCA5L	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40764600-40800600	Weak transcription	Psoas Muscle	Psoas
2	chr21:40778200-40816600	Weak transcription	Pancreas	Pancrea
3	chr21:40778400-40788200	Weak transcription	Fetal Brain Male	brain
4	chr21:40778400-40816600	Weak transcription	Left Ventricle	heart
5	chr21:40779200-40788800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr21:40779200-40801400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr21:40779800-40794000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr21:40779800-40794200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr21:40780200-40791000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr21:40780400-40802200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr21:40780600-40789800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr21:40780600-40790000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr21:40780600-40790600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr21:40780600-40794200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr21:40780600-40801800	Weak transcription	Lung	lung
16	chr21:40780800-40789200	Weak transcription	Fetal Intestine Small	intestine
17	chr21:40780800-40791800	Weak transcription	Brain Substantia Nigra	brain
18	chr21:40780800-40794200	Weak transcription	Brain Germinal Matrix	brain
19	chr21:40781000-40788000	Weak transcription	Primary T cells from cord blood	blood
20	chr21:40781000-40788000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr21:40781200-40798600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr21:40781200-40811000	Weak transcription	Aorta	Aorta
23	chr21:40781200-40813000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr21:40781200-40813200	Weak transcription	HSMMtube	muscle
25	chr21:40781400-40802000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr21:40785000-40800600	Weak transcription	Gastric	stomach
27	chr21:40786200-40792000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr21:40786400-40788000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr21:40786400-40788000	Weak transcription	Fetal Stomach	stomach
30	chr21:40786400-40792400	Weak transcription	Thymus	Thymus
31	chr21:40786600-40798000	Weak transcription	Ovary	ovary
32	chr21:40787800-40788600	Enhancers	K562	blood

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