Variant report

Variant	rs1899037
Chromosome Location	chr2:182128798-182128799
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10197170	0.94[ASN][1000 genomes]
rs1030964	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1371616	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1595812	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17365432	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1946895	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2033878	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4666738	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4666739	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62180205	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62180206	0.84[ASN][1000 genomes]
rs62180233	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62180234	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62180242	0.85[EUR][1000 genomes]
rs62180243	0.85[EUR][1000 genomes]
rs62180246	0.85[EUR][1000 genomes]
rs62180252	0.85[EUR][1000 genomes]
rs6706833	0.94[ASN][1000 genomes]
rs7566314	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs976461	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1002647	chr2:182078521-182392273	Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv536064	chr2:182078521-182392273	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1899037	TSPYL5	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182117800-182140200	Weak transcription	Dnd41	blood
2	chr2:182117800-182140600	Weak transcription	Fetal Thymus	thymus
3	chr2:182118000-182128800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:182126200-182129000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr2:182126400-182129200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:182127600-182129000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:182127800-182129000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:182128000-182133400	Weak transcription	HSMMtube	muscle
9	chr2:182128000-182134600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:182128000-182135000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:182128400-182139800	Weak transcription	Primary T cells from cord blood	blood
12	chr2:182128400-182139800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:182128600-182129000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:182128600-182129000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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