Variant report

Variant	rs1541815
Chromosome Location	chr5:36702290-36702291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36701247..36704029-chr5:36711185..36713020,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf42-3	chr5:36700875-36703066	NONHSAT101040

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1019769	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1019770	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033225	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36683	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7716616	0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541815	SLC1A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 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	chr5:36693800-36702800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:36700200-36724200	Weak transcription	Primary T cells from cord blood	blood
7	chr5:36700800-36702800	Enhancers	Primary B cells from peripheral blood	blood
8	chr5:36701000-36702800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:36701000-36704800	Enhancers	Fetal Lung	lung
10	chr5:36701200-36702400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:36701400-36706600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:36701400-36706600	Weak transcription	Spleen	Spleen
13	chr5:36701400-36707000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:36701400-36707400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:36701600-36702800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:36701600-36704000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:36701800-36702800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:36701800-36703400	Weak transcription	Adipose Nuclei	Adipose
19	chr5:36702000-36702400	Flanking Active TSS	Fetal Heart	heart
20	chr5:36702000-36703000	Genic enhancers	Primary B cells from cord blood	blood
21	chr5:36702000-36703200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr5:36702000-36703400	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:36702200-36702400	Genic enhancers	GM12878-XiMat	blood
24	chr5:36702200-36702800	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links