Variant report

Variant	rs2376179
Chromosome Location	chr17:33847026-33847027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF4	chr17:33847025-33847464	GM12878	blood:	n/a	n/a
2	IRF4	chr17:33846968-33847517	GM12878	blood:	n/a	n/a
3	PAX5	chr17:33846984-33847457	GM12878	blood:	n/a	n/a
4	NFIC	chr17:33846989-33847473	GM12878	blood:	n/a	n/a
5	FOXM1	chr17:33846990-33847445	GM12878	blood:	n/a	n/a
6	CTCF	chr17:33846960-33847110	GM12866	blood:	n/a	n/a
7	BATF	chr17:33846924-33847412	GM12878	blood:	n/a	n/a
8	RUNX3	chr17:33846898-33847432	GM12878	blood:	n/a	n/a
9	BCL11A	chr17:33847021-33847496	GM12878	blood:	n/a	n/a
10	TCF7L2	chr17:33846862-33847323	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
ENSG00000255987	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs4796094	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4796095	0.88[CEU][hapmap]
rs4796096	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6505478	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6505480	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6505482	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7221507	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7405475	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8067329	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8077695	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs986419	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915940	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active 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 miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv519981	chr17:33841737-33864479	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv574754	chr17:33841737-33881631	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2376179	TBC1D29	cis	cerebellum	SCAN
rs2376179	SGK494	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33835400-33849600	Weak transcription	Spleen	Spleen
2	chr17:33842400-33847200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:33842800-33848200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr17:33843200-33852200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr17:33846000-33847200	ZNF genes & repeats	GM12878-XiMat	blood
6	chr17:33846000-33848200	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr17:33846000-33848200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:33846000-33848200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:33846000-33848600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:33846200-33847200	Enhancers	Duodenum Mucosa	Duodenum
11	chr17:33846200-33847400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr17:33846200-33849600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr17:33846400-33847200	Enhancers	Stomach Mucosa	stomach
14	chr17:33846400-33852000	Enhancers	Primary T cells from cord blood	blood
15	chr17:33846600-33847200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr17:33846600-33847600	Bivalent Enhancer	Fetal Lung	lung
17	chr17:33846600-33849200	Genic enhancers	Dnd41	blood
18	chr17:33846800-33847200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:33846800-33847400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr17:33846800-33847400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
21	chr17:33846800-33848400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr17:33846800-33851600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr17:33847000-33847600	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr17:33847000-33848400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr17:33847000-33848400	Weak transcription	HMEC	breast
26	chr17:33847000-33848600	Weak transcription	NHEK	skin
27	chr17:33847000-33849200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links