Variant report

Variant	rs4062989
Chromosome Location	chr2:96481071-96481072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANKRD36C-1	chr2:96479798-96482510	NONHSAT072510
2	lnc-ANKRD36C-1	chr2:96479798-96482417	NONHSAT072514
3	lnc-ANKRD36C-1	chr2:96479798-96486944	NONHSAT072513

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1043092	0.86[EUR][1000 genomes]
rs11164053	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11676926	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11683523	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11687113	0.86[CEU][hapmap]
rs11689832	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11690061	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11691090	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11695514	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12477206	0.82[AMR][1000 genomes]
rs1813381	0.83[EUR][1000 genomes]
rs1974770	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2315421	0.83[EUR][1000 genomes]
rs2438978	0.95[CEU][hapmap]
rs2462774	0.93[CEU][hapmap]
rs2579519	0.86[CEU][hapmap]
rs34639392	0.82[EUR][1000 genomes]
rs3855810	0.85[EUR][1000 genomes]
rs3968756	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4062840	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4063021	0.81[EUR][1000 genomes]
rs4332959	0.80[EUR][1000 genomes]
rs4527246	0.87[CEU][hapmap]
rs4907217	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4907219	0.86[AMR][1000 genomes]
rs4907224	0.87[AMR][1000 genomes]
rs4907288	0.87[CEU][hapmap]
rs59076415	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62153670	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62153678	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62153692	0.91[AMR][1000 genomes]
rs62155750	0.91[EUR][1000 genomes]
rs6706905	0.83[EUR][1000 genomes]
rs6717101	0.82[EUR][1000 genomes]
rs6719831	0.83[EUR][1000 genomes]
rs6740563	0.86[CEU][hapmap]
rs72823920	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1003371	chr2:96326106-96684876	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv874662	chr2:96334397-96578621	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv874664	chr2:96370571-96534132	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv874665	chr2:96370571-96596515	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv874666	chr2:96370571-96691125	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1004482	chr2:96408987-96596717	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv834303	chr2:96432935-96551704	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv428054	chr2:96438238-96627125	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv961832	chr2:96453677-96671971	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv874667	chr2:96465201-96596515	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv874668	chr2:96465201-96600569	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv1826589	chr2:96468292-96583910	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv1826305	chr2:96468492-96583710	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
17	esv1848259	chr2:96477989-96583252	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4062989	GPAT2	cis	Adipose Subcutaneous	GTEx
rs4062989	ADRA2B	cis	Thyroid	GTEx
rs4062989	ADRA2B	cis	Nerve Tibial	GTEx
rs4062989	FAHD2CP	cis	lung	GTEx
rs4062989	GPAT2	cis	Muscle Skeletal	GTEx
rs4062989	FAHD2CP	cis	Muscle Skeletal	GTEx
rs4062989	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs4062989	FAHD2CP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96468200-96481400	Weak transcription	Fetal Brain Male	brain
2	chr2:96470000-96481800	Weak transcription	Primary T cells from cord blood	blood
3	chr2:96470600-96482400	Weak transcription	Fetal Stomach	stomach
4	chr2:96471200-96482000	Weak transcription	Fetal Lung	lung
5	chr2:96471200-96482200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:96471600-96482200	Weak transcription	Dnd41	blood
7	chr2:96472600-96482000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:96473800-96483400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:96476200-96482000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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