Variant report

Variant	rs61401688
Chromosome Location	chr5:49964905-49964906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49963990..49965571-chr5:49984249..49987060,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10471414	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10737958	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11954386	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12055210	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12153387	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12186752	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1375128	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs152001	0.87[EUR][1000 genomes]
rs154136	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs166863	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs204915	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2354533	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404958	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2463796	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2463797	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2594708	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26072	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs27243	0.89[EUR][1000 genomes]
rs27255	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs27598	0.86[EUR][1000 genomes]
rs27934	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs27964	0.88[EUR][1000 genomes]
rs282544	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs282548	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282555	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282556	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs282560	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2883460	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs32396	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36077571	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3864235	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4548483	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55932149	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56670602	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62366908	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62366910	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62366941	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450384	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6450391	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66912405	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7717033	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers 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	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv818352	chr5:49958221-50017724	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv968172	chr5:49961360-49966431	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv968910	chr5:49961360-49980983	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs61401688	PARP8	cis	Adipose Subcutaneous	GTEx
rs61401688	PARP8	cis	Thyroid	GTEx
rs61401688	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs61401688	PARP8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49961600-49965200	Active TSS	GM12878-XiMat	blood
2	chr5:49961600-49965400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:49961800-49965000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr5:49961800-49965000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr5:49961800-49965400	Active TSS	Thymus	Thymus
6	chr5:49961800-49965400	Active TSS	HMEC	breast
7	chr5:49962000-49965000	Active TSS	Primary monocytes fromperipheralblood	blood
8	chr5:49962000-49965000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr5:49962000-49965200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:49962000-49965200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:49962200-49965200	Active TSS	Primary T cells fromperipheralblood	blood
12	chr5:49962200-49965200	Active TSS	Stomach Smooth Muscle	stomach
13	chr5:49963400-49965600	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr5:49963400-49965800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:49963400-49965800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr5:49963600-49965400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:49964000-49965200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr5:49964000-49965600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:49964200-49966400	Weak transcription	Psoas Muscle	Psoas
20	chr5:49964200-49968000	Weak transcription	Spleen	Spleen
21	chr5:49964400-49965400	Enhancers	Colon Smooth Muscle	Colon
22	chr5:49964400-49965400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:49964400-49965400	Enhancers	Small Intestine	intestine
24	chr5:49964400-49966000	Flanking Active TSS	Dnd41	blood
25	chr5:49964400-49967800	Weak transcription	Stomach Mucosa	stomach
26	chr5:49964400-49968000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:49964400-49970000	Weak transcription	Aorta	Aorta
28	chr5:49964400-49975400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:49964400-49977400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:49964400-49982400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:49964400-49983400	Weak transcription	Esophagus	oesophagus
32	chr5:49964600-49965000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr5:49964600-49965000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr5:49964600-49965000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr5:49964600-49965000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr5:49964600-49965600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr5:49964600-49965600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr5:49964600-49965600	Flanking Active TSS	NHEK	skin
39	chr5:49964600-49965800	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr5:49964600-49965800	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr5:49964600-49965800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr5:49964600-49966000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr5:49964600-49966000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr5:49964600-49966200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:49964600-49966200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr5:49964600-49969000	Weak transcription	Osteobl	bone
47	chr5:49964800-49965000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:49964800-49965000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:49964800-49965000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:49964800-49965000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links