Variant report

Variant	rs1933105
Chromosome Location	chr1:168526394-168526395
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1024176	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024177	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753777	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10918924	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10918925	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10918926	0.97[ASN][1000 genomes]
rs1123864	0.89[ASN][1000 genomes]
rs12021763	0.89[ASN][1000 genomes]
rs12049040	0.89[ASN][1000 genomes]
rs12409982	0.89[ASN][1000 genomes]
rs12568619	0.89[ASN][1000 genomes]
rs1933100	0.96[ASN][1000 genomes]
rs1933104	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1933109	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933110	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933112	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1933114	0.95[ASN][1000 genomes]
rs2179500	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2223583	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34328291	0.89[ASN][1000 genomes]
rs3820405	0.93[ASN][1000 genomes]
rs3820411	0.82[ASN][1000 genomes]
rs3982407	0.85[ASN][1000 genomes]
rs3982408	0.86[ASN][1000 genomes]
rs4276892	0.84[EUR][1000 genomes]
rs4656605	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475361	0.88[ASN][1000 genomes]
rs7514168	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516427	0.83[ASN][1000 genomes]
rs7518740	0.85[ASN][1000 genomes]
rs7518803	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014626	chr1:168441288-168642731	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535196	chr1:168441288-168642731	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1011821	chr1:168441488-168642592	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv535197	chr1:168441488-168642592	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1008852	chr1:168449940-168643905	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv535198	chr1:168449940-168643905	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	esv1792733	chr1:168526394-168544716	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1933105	XCL2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168522000-168527400	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr1:168523000-168526400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:168523000-168527200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr1:168523000-168527600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:168524800-168526800	Weak transcription	A549	lung
6	chr1:168525400-168526600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr1:168525400-168526600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:168525400-168526800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:168525400-168527600	Enhancers	HepG2	liver
10	chr1:168526000-168526600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:168526000-168526800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:168526000-168527400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:168526200-168526400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:168526200-168527000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:168526200-168527000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:168526200-168527000	Enhancers	HMEC	breast
17	chr1:168526200-168527600	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links