Variant report

Variant	rs2929516
Chromosome Location	chr15:72338423-72338424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10851849	1.00[EUR][1000 genomes]
rs11072348	1.00[EUR][1000 genomes]
rs11072352	1.00[EUR][1000 genomes]
rs12438985	1.00[TSI][hapmap]
rs12903688	1.00[EUR][1000 genomes]
rs1457030	1.00[EUR][1000 genomes]
rs1598714	1.00[EUR][1000 genomes]
rs2254976	0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2415131	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2625531	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2723338	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2742321	1.00[EUR][1000 genomes]
rs28552371	1.00[CEU][hapmap]
rs2856926	1.00[EUR][1000 genomes]
rs2912208	1.00[EUR][1000 genomes]
rs2912209	1.00[EUR][1000 genomes]
rs2912211	1.00[EUR][1000 genomes]
rs2912212	1.00[EUR][1000 genomes]
rs2912213	1.00[EUR][1000 genomes]
rs2912232	1.00[EUR][1000 genomes]
rs2925647	1.00[EUR][1000 genomes]
rs2925651	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs2929520	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2929523	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2957363	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap]
rs2957367	1.00[EUR][1000 genomes]
rs2957370	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2957371	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs2957722	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2959901	1.00[EUR][1000 genomes]
rs2959902	1.00[EUR][1000 genomes]
rs2959907	1.00[EUR][1000 genomes]
rs2959936	1.00[EUR][1000 genomes]
rs2959937	1.00[EUR][1000 genomes]
rs2959942	1.00[EUR][1000 genomes]
rs35293819	1.00[EUR][1000 genomes]
rs4238451	1.00[EUR][1000 genomes]
rs4461029	1.00[EUR][1000 genomes]
rs4776587	1.00[EUR][1000 genomes]
rs4776588	1.00[EUR][1000 genomes]
rs4777487	1.00[EUR][1000 genomes]
rs4777493	1.00[EUR][1000 genomes]
rs56168468	1.00[EUR][1000 genomes]
rs6494988	1.00[EUR][1000 genomes]
rs6494989	1.00[EUR][1000 genomes]
rs6494995	1.00[EUR][1000 genomes]
rs7170173	1.00[EUR][1000 genomes]
rs7171097	1.00[EUR][1000 genomes]
rs7173348	1.00[EUR][1000 genomes]
rs7173532	1.00[EUR][1000 genomes]
rs7177512	1.00[EUR][1000 genomes]
rs7179691	1.00[EUR][1000 genomes]
rs7180934	1.00[EUR][1000 genomes]
rs8031658	1.00[EUR][1000 genomes]
rs8034892	1.00[EUR][1000 genomes]
rs8192347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap]
rs930871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[EUR][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	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
6	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2929516	PARP6	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72226800-72343600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr15:72280200-72338800	Weak transcription	Hela-S3	cervix
3	chr15:72282000-72341800	Weak transcription	Brain Angular Gyrus	brain
4	chr15:72282200-72338800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:72282800-72347000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:72282800-72349800	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:72298400-72344000	Weak transcription	Spleen	Spleen
8	chr15:72300000-72351000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:72300200-72341800	Weak transcription	Brain Substantia Nigra	brain
10	chr15:72301000-72341800	Weak transcription	Brain Anterior Caudate	brain
11	chr15:72301000-72361200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:72302200-72349400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:72311600-72341800	Weak transcription	Fetal Kidney	kidney
14	chr15:72326600-72340000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:72326600-72341000	Weak transcription	NHLF	lung
16	chr15:72326600-72341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:72326600-72342200	Weak transcription	Fetal Brain Male	brain
18	chr15:72326600-72343600	Weak transcription	Right Ventricle	heart
19	chr15:72328400-72338600	Weak transcription	HepG2	liver
20	chr15:72328400-72349800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:72329000-72339000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:72329200-72339200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:72329800-72339400	Weak transcription	NH-A	brain
24	chr15:72329800-72340000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:72330000-72343400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:72330000-72349800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:72330000-72349800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:72330200-72339600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:72330200-72341000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:72330400-72339200	Weak transcription	Osteobl	bone
31	chr15:72331000-72344200	Weak transcription	GM12878-XiMat	blood
32	chr15:72331200-72343600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:72332200-72342200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:72332400-72343600	Weak transcription	Gastric	stomach
35	chr15:72332600-72343400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:72332600-72343800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:72332800-72340200	Weak transcription	Psoas Muscle	Psoas
38	chr15:72332800-72340200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:72332800-72341000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:72332800-72341800	Weak transcription	Fetal Heart	heart
41	chr15:72332800-72343400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr15:72332800-72343600	Weak transcription	Fetal Intestine Small	intestine
43	chr15:72333000-72343600	Weak transcription	Brain Germinal Matrix	brain
44	chr15:72333200-72353800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr15:72334000-72341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:72334000-72355000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:72334200-72343600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:72334200-72343600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:72334400-72350000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:72335200-72339400	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links