Variant report

Variant	rs17778487
Chromosome Location	chr5:100114085-100114086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10478648	0.92[AMR][1000 genomes]
rs17159001	0.89[EUR][1000 genomes]
rs17160818	0.91[AMR][1000 genomes]
rs17719528	0.83[AMR][1000 genomes]
rs17720901	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17721341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17721790	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17722713	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17722756	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17723146	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17725086	1.00[AMR][1000 genomes]
rs17725882	1.00[AMR][1000 genomes]
rs17726376	1.00[AMR][1000 genomes]
rs17775827	0.83[AMR][1000 genomes]
rs17775983	0.83[AMR][1000 genomes]
rs17776515	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17776916	0.85[EUR][1000 genomes]
rs17777079	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17777349	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17778120	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778598	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17779305	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17779694	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17779731	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17780072	1.00[AMR][1000 genomes]
rs17780121	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs17780854	1.00[AMR][1000 genomes]
rs17780992	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs17781289	1.00[AMR][1000 genomes]
rs17782650	1.00[AMR][1000 genomes]
rs57652761	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6866516	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73777435	1.00[AMR][1000 genomes]
rs73777437	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	esv2762532	chr5:100041758-100136552	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17778487	SCGB2A2	trans	brain	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100111400-100114400	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr5:100111400-100114400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:100111400-100114800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr5:100113000-100114200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:100113000-100114200	Enhancers	Primary T cells from cord blood	blood
6	chr5:100113000-100114200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:100113000-100114200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:100113000-100114200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:100113400-100114200	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr5:100113400-100116000	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:100113600-100115600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:100113800-100114200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:100113800-100114200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:100113800-100114200	Enhancers	A549	lung
15	chr5:100113800-100114200	Enhancers	NHEK	skin
16	chr5:100113800-100114400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:100113800-100114400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:100113800-100115200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:100113800-100115600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:100113800-100115600	Enhancers	Dnd41	blood
21	chr5:100114000-100114200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:100114000-100114200	Enhancers	Primary hematopoietic stem cells	blood
23	chr5:100114000-100114200	Enhancers	NH-A	brain
24	chr5:100114000-100114400	Enhancers	Hela-S3	cervix
25	chr5:100114000-100114400	Enhancers	HUVEC	blood vessel
26	chr5:100114000-100115200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr5:100114000-100115200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:100114000-100115400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:100114000-100115400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:100114000-100115400	Weak transcription	Adipose Nuclei	Adipose
31	chr5:100114000-100115400	Enhancers	GM12878-XiMat	blood
32	chr5:100114000-100115600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:100114000-100115600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:100114000-100115800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr5:100114000-100116000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr5:100114000-100136400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links