Variant report

Variant	rs1019770
Chromosome Location	chr5:36700538-36700539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1019769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541815	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033225	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36683	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7716616	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv830263	chr5:36576504-36755093	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv880571	chr5:36675699-36710205	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1019770	CAPSL	cis	cerebellum	SCAN
rs1019770	SLC1A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36690600-36702800	Weak transcription	Aorta	Aorta
2	chr5:36693200-36703400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:36693400-36702800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:36693400-36703400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:36693800-36700800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr5:36693800-36701200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:36693800-36701400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:36693800-36701400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:36693800-36701600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:36693800-36702800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:36696000-36701200	Weak transcription	Spleen	Spleen
12	chr5:36697600-36700800	Enhancers	Fetal Heart	heart
13	chr5:36698800-36701600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:36699200-36701200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:36700000-36701000	Weak transcription	Primary B cells from cord blood	blood
16	chr5:36700000-36701000	Weak transcription	Fetal Lung	lung
17	chr5:36700200-36701200	Genic enhancers	GM12878-XiMat	blood
18	chr5:36700200-36701800	Strong transcription	Primary hematopoietic stem cells	blood
19	chr5:36700200-36724200	Weak transcription	Primary T cells from cord blood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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