Variant report

Variant	rs12378604
Chromosome Location	chr9:73865536-73865537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf85-8	chr9:73865406-73865546	l_3783_chr9:73865405-73895070_testes

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10868991	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10868995	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10868997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142711	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11142717	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11142736	0.89[EUR][1000 genomes]
rs11142750	0.91[EUR][1000 genomes]
rs11142753	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142763	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11142773	0.90[EUR][1000 genomes]
rs11142774	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142777	0.85[EUR][1000 genomes]
rs11142778	0.85[EUR][1000 genomes]
rs11142779	0.84[EUR][1000 genomes]
rs11142780	0.84[EUR][1000 genomes]
rs11142781	0.84[EUR][1000 genomes]
rs12005021	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12379392	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380581	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1504388	0.83[EUR][1000 genomes]
rs1504389	0.83[EUR][1000 genomes]
rs1504390	0.83[EUR][1000 genomes]
rs1504391	0.83[EUR][1000 genomes]
rs1504392	0.83[EUR][1000 genomes]
rs1504404	0.91[EUR][1000 genomes]
rs1532801	0.83[EUR][1000 genomes]
rs1532802	0.83[EUR][1000 genomes]
rs1532804	0.83[EUR][1000 genomes]
rs17056425	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17056483	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17616798	0.91[EUR][1000 genomes]
rs2174308	0.89[EUR][1000 genomes]
rs2309916	0.83[EUR][1000 genomes]
rs4079469	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4370599	0.83[EUR][1000 genomes]
rs7018911	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7021834	0.90[EUR][1000 genomes]
rs7027219	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7039341	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7040929	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043726	0.90[EUR][1000 genomes]
rs73467746	0.89[EUR][1000 genomes]
rs73469317	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73469327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73647995	0.90[EUR][1000 genomes]
rs73647997	0.88[ASN][1000 genomes]
rs73647998	0.88[ASN][1000 genomes]
rs73648000	0.88[ASN][1000 genomes]
rs73648001	0.88[ASN][1000 genomes]
rs73649703	0.88[ASN][1000 genomes]
rs73649705	0.88[ASN][1000 genomes]
rs73649709	0.86[ASN][1000 genomes]
rs763359	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7848661	0.90[EUR][1000 genomes]
rs7854181	0.83[EUR][1000 genomes]
rs7854330	0.85[EUR][1000 genomes]
rs7870153	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9785216	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9785312	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985654	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035505	chr9:73709852-73934353	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv893442	chr9:73778502-74115344	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1052375	chr9:73793681-73893133	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv540152	chr9:73793681-73893133	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv430073	chr9:73825109-73869960	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv430074	chr9:73825109-73870395	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv893443	chr9:73859086-74008905	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv916062	chr9:73861614-74246247	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73863600-73866200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:73864400-73866000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:73864400-73866400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr9:73864600-73866000	Enhancers	Liver	Liver
5	chr9:73864600-73866200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr9:73864600-73866400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:73864800-73865600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr9:73864800-73866200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr9:73864800-73867600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:73865000-73865800	Enhancers	Fetal Intestine Large	intestine
11	chr9:73865200-73865600	Enhancers	H9 Cell Line	embryonic stem cell
12	chr9:73865200-73866000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr9:73865200-73866000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:73865400-73865600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr9:73865400-73865600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr9:73865400-73865600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr9:73865400-73865600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:73865400-73865800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:73865400-73865800	Enhancers	Fetal Kidney	kidney
20	chr9:73865400-73866000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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