Variant report

Variant	rs497490
Chromosome Location	chr1:160744961-160744962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLAMF7-1	chr1:160743317-160745088	ENSG00000250225

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs521925	0.93[AFR][1000 genomes]
rs549471	0.84[MEX][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	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428532	chr1:160671125-160767708	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv947134	chr1:160742631-160749214	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs497490	FCRL1	cis	cerebellum	SCAN
rs497490	FDPS	cis	cerebellum	SCAN
rs497490	CLK2	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160738200-160745200	Weak transcription	Primary B cells from cord blood	blood
2	chr1:160738400-160747400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:160743200-160747400	Enhancers	GM12878-XiMat	blood
4	chr1:160743800-160745200	Weak transcription	Esophagus	oesophagus
5	chr1:160744200-160745200	Enhancers	NHEK	skin
6	chr1:160744400-160746400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:160744600-160745200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:160744600-160745400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:160744600-160745600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:160744600-160745600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:160744600-160746000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:160744800-160745000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:160744800-160745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:160744800-160745200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:160744800-160745200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:160744800-160745200	Enhancers	Dnd41	blood
17	chr1:160744800-160745400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:160744800-160745400	Enhancers	Primary T cells from cord blood	blood
19	chr1:160744800-160745400	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:160744800-160745400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:160744800-160745400	Enhancers	HMEC	breast
22	chr1:160744800-160745600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:160744800-160745600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr1:160744800-160746000	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr1:160744800-160747800	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links