Variant report

Variant	rs6559680
Chromosome Location	chr9:85359392-85359393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RASEF-2	chr9:85358982-85359707	NONHSAT132726

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11139702	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11139703	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11139704	0.92[ASN][1000 genomes]
rs11139705	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11139707	0.92[ASN][1000 genomes]
rs11139708	0.93[ASN][1000 genomes]
rs11139709	0.92[ASN][1000 genomes]
rs11139711	0.95[ASN][1000 genomes]
rs11139716	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs11139717	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11139722	0.98[ASN][1000 genomes]
rs11139723	0.94[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs12236312	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1332473	0.92[ASN][1000 genomes]
rs17085735	0.92[ASN][1000 genomes]
rs4510939	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62579110	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62579111	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62579112	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62579113	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62579114	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62579115	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62579116	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62579117	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62579137	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62579139	0.95[AFR][1000 genomes]
rs72737494	0.92[ASN][1000 genomes]
rs72737498	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72739125	0.97[ASN][1000 genomes]
rs7869575	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428539	chr9:85240027-85402367	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1035314	chr9:85348780-85549246	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv540161	chr9:85348780-85549246	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1039930	chr9:85349993-85536746	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1002297	chr9:85351450-85360245	Enhancers Weak transcription Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85348200-85361400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:85349800-85361600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:85350000-85364600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:85352200-85361200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:85352200-85364800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:85352400-85361600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:85353000-85361600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:85353200-85361600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:85355200-85359800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:85356200-85364400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr9:85358200-85361400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr9:85358400-85361600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:85359000-85359400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:85359000-85360800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:85359000-85362400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:85359200-85361400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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