Variant report

Variant	rs3108112
Chromosome Location	chr2:34949994-34949995
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RASGRP3-4	chr2:34947066-34950118	NONHSAT070045

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11124397	0.83[AFR][1000 genomes]
rs11897499	0.84[ASN][1000 genomes]
rs11897621	0.84[ASN][1000 genomes]
rs12712403	0.81[AFR][1000 genomes]
rs2049638	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2888058	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108102	0.83[ASN][1000 genomes]
rs3108103	0.82[ASN][1000 genomes]
rs3108104	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3108107	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3108108	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3108109	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108110	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108115	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3108116	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3115233	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3115236	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3115237	0.88[ASN][1000 genomes]
rs3115238	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3115239	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3115249	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3115250	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3115267	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999091	chr2:34154486-34993188	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv535629	chr2:34154486-34993188	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv873804	chr2:34156867-35047107	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv873810	chr2:34456200-35047107	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1002396	chr2:34581285-34993188	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv535633	chr2:34581285-34993188	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv873821	chr2:34738616-35416075	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1003361	chr2:34746445-35202302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1000535	chr2:34831613-34986940	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv535634	chr2:34831613-34986940	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873825	chr2:34892832-35115848	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1003322	chr2:34898412-35216795	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv581375	chr2:34912850-35032910	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
14	nsv873826	chr2:34915314-34986833	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	nsv873827	chr2:34919515-34962533	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
16	nsv873828	chr2:34919515-35022419	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
17	nsv1010863	chr2:34922329-35052108	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
18	nsv1002915	chr2:34923003-35052108	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
19	nsv873829	chr2:34928080-35022419	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
20	nsv998914	chr2:34944923-34964450	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
21	nsv430679	chr2:34946679-35025804	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:34926400-34957600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:34939800-34952800	Weak transcription	Liver	Liver
3	chr2:34949800-34950400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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