Variant report

Variant	rs12555636
Chromosome Location	chr9:99925034-99925035
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTSL2-4	chr9:99924847-99925128	ENSG00000159712.9

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10521028	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10980890	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10980955	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981005	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981158	0.81[AMR][1000 genomes]
rs10981161	0.85[AMR][1000 genomes]
rs12377244	0.86[AMR][1000 genomes]
rs12378555	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12550862	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1857085	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34592472	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35285539	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4014782	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4128763	0.93[JPT][hapmap]
rs56860287	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58003970	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7848439	0.81[AMR][1000 genomes]
rs7851025	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7860303	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7865758	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv972432	chr9:99874607-99958095	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv969695	chr9:99924101-99925101	Weak transcription Strong transcription	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99911600-99957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:99913400-99930800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:99913600-99930800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:99918000-99946800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:99921400-99948800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:99922000-99937800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:99922800-99926200	Weak transcription	Dnd41	blood
8	chr9:99923600-99932200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:99923600-99938000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:99923800-99927000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:99923800-99936200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:99924200-99925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:99924200-99926600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:99924400-99926000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:99924600-99926000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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