Variant report

Variant	rs2837012
Chromosome Location	chr21:40784310-40784311
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40762468..40764445-chr21:40783033..40785602,2	K562	blood:
2	chr21:40783103..40784656-chr21:40785669..40787209,3	MCF-7	breast:
3	chr21:40759292..40761069-chr21:40781933..40784921,2	MCF-7	breast:
4	chr21:40784167..40788125-chr21:40789270..40793629,5	K562	blood:
5	chr21:40784172..40786571-chr21:40796585..40798717,2	K562	blood:
6	chr21:40782804..40784995-chr21:40816330..40818172,2	K562	blood:
7	chr21:40784043..40786943-chr21:40818304..40821060,2	K562	blood:

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

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11088475	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2049823	0.86[JPT][hapmap]
rs2837010	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837011	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837013	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837014	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2837016	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]
rs2837027	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2837028	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2837033	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2837038	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4816628	0.86[JPT][hapmap]
rs7276842	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7277602	0.87[JPT][hapmap]
rs8129564	0.84[ASN][1000 genomes]
rs8130381	0.94[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs9979289	0.86[JPT][hapmap]
rs9979353	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9983180	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9983435	0.82[CHB][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	esv3355532	chr21:40783721-40786949	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2837012	LCA5L	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40764600-40800600	Weak transcription	Psoas Muscle	Psoas
2	chr21:40768200-40784600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr21:40770200-40785800	Weak transcription	Esophagus	oesophagus
4	chr21:40772600-40786400	Weak transcription	Fetal Heart	heart
5	chr21:40776600-40786200	Weak transcription	K562	blood
6	chr21:40778200-40816600	Weak transcription	Pancreas	Pancrea
7	chr21:40778400-40784400	Weak transcription	NHDF-Ad	bronchial
8	chr21:40778400-40787200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr21:40778400-40787200	Weak transcription	NHEK	skin
10	chr21:40778400-40787400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr21:40778400-40787400	Weak transcription	HSMM	muscle
12	chr21:40778400-40787800	Weak transcription	Spleen	Spleen
13	chr21:40778400-40788200	Weak transcription	Fetal Brain Male	brain
14	chr21:40778400-40816600	Weak transcription	Left Ventricle	heart
15	chr21:40778800-40784400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr21:40779200-40784800	Weak transcription	Gastric	stomach
17	chr21:40779200-40785800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr21:40779200-40788800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr21:40779200-40801400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr21:40779800-40794000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr21:40779800-40794200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr21:40780000-40784400	Weak transcription	Fetal Lung	lung
23	chr21:40780200-40784400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr21:40780200-40786400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr21:40780200-40791000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr21:40780400-40784600	Weak transcription	Fetal Intestine Large	intestine
27	chr21:40780400-40785600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr21:40780400-40786400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr21:40780400-40802200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr21:40780600-40784400	Weak transcription	Ovary	ovary
31	chr21:40780600-40784600	Weak transcription	Brain Anterior Caudate	brain
32	chr21:40780600-40786800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr21:40780600-40787400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr21:40780600-40787800	Weak transcription	Adipose Nuclei	Adipose
35	chr21:40780600-40787800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr21:40780600-40789800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr21:40780600-40790000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr21:40780600-40790600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr21:40780600-40794200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr21:40780600-40801800	Weak transcription	Lung	lung
41	chr21:40780800-40787400	Weak transcription	Fetal Brain Female	brain
42	chr21:40780800-40787400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr21:40780800-40789200	Weak transcription	Fetal Intestine Small	intestine
44	chr21:40780800-40791800	Weak transcription	Brain Substantia Nigra	brain
45	chr21:40780800-40794200	Weak transcription	Brain Germinal Matrix	brain
46	chr21:40781000-40788000	Weak transcription	Primary T cells from cord blood	blood
47	chr21:40781000-40788000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr21:40781200-40785800	Weak transcription	Thymus	Thymus
49	chr21:40781200-40787600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr21:40781200-40787800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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