Variant report

Variant	rs1988613
Chromosome Location	chr5:49959073-49959074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EMB-7	chr5:49958693-49959100	ENSG00000271752.1

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10038842	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039639	0.90[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041633	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10043477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045122	1.00[ASN][1000 genomes]
rs10052001	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10065069	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10070517	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071272	1.00[ASN][1000 genomes]
rs10434558	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10471888	1.00[ASN][1000 genomes]
rs10471893	1.00[ASN][1000 genomes]
rs10471940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471956	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10755235	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10940472	0.93[EUR][1000 genomes]
rs10940497	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11739828	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11741205	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11750241	0.93[EUR][1000 genomes]
rs11750771	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12188262	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12188654	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12518710	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12519006	0.87[EUR][1000 genomes]
rs12521579	0.87[EUR][1000 genomes]
rs12654776	0.82[EUR][1000 genomes]
rs13153982	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13159764	0.82[AFR][1000 genomes]
rs13162921	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13164951	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13173734	0.93[EUR][1000 genomes]
rs13355372	1.00[ASN][1000 genomes]
rs13355434	1.00[ASN][1000 genomes]
rs13359044	0.87[EUR][1000 genomes]
rs1375127	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152102	0.87[EUR][1000 genomes]
rs154133	0.87[EUR][1000 genomes]
rs154135	0.86[EUR][1000 genomes]
rs154137	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs154138	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs154141	0.87[EUR][1000 genomes]
rs157970	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs16884018	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs169497	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs171555	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17195388	0.87[EUR][1000 genomes]
rs182230	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1823262	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1839128	0.91[CEU][hapmap]
rs2034392	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2034394	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2354526	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2548581	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2548582	0.86[EUR][1000 genomes]
rs2548583	0.86[EUR][1000 genomes]
rs256340	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs256341	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs26062	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs26065	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs26066	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26068	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26069	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs26071	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2697662	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27156	0.82[EUR][1000 genomes]
rs27244	0.85[EUR][1000 genomes]
rs27245	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs27251	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs27254	0.85[EUR][1000 genomes]
rs27357	0.83[EUR][1000 genomes]
rs27465	0.86[EUR][1000 genomes]
rs27467	1.00[CEU][hapmap]
rs27468	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs27469	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs27574	0.82[EUR][1000 genomes]
rs27627	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs27725	0.83[EUR][1000 genomes]
rs28085	0.83[EUR][1000 genomes]
rs282549	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282550	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs282551	0.86[EUR][1000 genomes]
rs282552	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs282553	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs282557	0.93[EUR][1000 genomes]
rs282559	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282561	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs32377	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32378	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32404	1.00[CEU][hapmap]
rs32425	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3763367	0.99[EUR][1000 genomes]
rs39613	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4029420	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4101529	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs42284	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4865628	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4865846	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4865974	1.00[JPT][hapmap]
rs4866001	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs57079776	0.93[EUR][1000 genomes]
rs578198	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs62366937	0.96[EUR][1000 genomes]
rs6450301	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6450359	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869356	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872496	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6879306	1.00[ASN][1000 genomes]
rs6886872	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888147	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6890519	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6890869	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs73093361	1.00[ASN][1000 genomes]
rs73112331	1.00[ASN][1000 genomes]
rs73112340	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7449019	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709831	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7710150	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7711839	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723361	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7728222	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7730847	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7734389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895801	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1988613	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs1988613	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49949800-49961600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:49950000-49959400	Weak transcription	Primary T cells from cord blood	blood
3	chr5:49950200-49959200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:49953000-49959400	Weak transcription	Stomach Mucosa	stomach
5	chr5:49953000-49961800	Weak transcription	Esophagus	oesophagus
6	chr5:49954400-49959200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:49954400-49961000	Weak transcription	Primary B cells from cord blood	blood
8	chr5:49958800-49959200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr5:49958800-49961800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:49959000-49959800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links