Variant report

Variant	rs11792489
Chromosome Location	chr9:103224064-103224065
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103218360..103221839-chr9:103223201..103225768,3	MCF-7	breast:
2	chr9:103216500..103219242-chr9:103223306..103224968,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf30-3	chr9:103221120-103224907	ncRnaDb_ncrna_FR405056_1

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11788011	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11788350	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11788918	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11789665	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11790432	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11791916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs11792747	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11792926	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11793144	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11793359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11793457	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11794817	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13283467	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13284662	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13286180	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13289939	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13292364	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13293829	1.00[YRI][hapmap]
rs13294866	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13301847	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13302460	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28759503	0.80[AMR][1000 genomes]
rs34138998	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34169031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34234519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34390257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34555593	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34759817	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34779059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34798346	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34999135	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35039632	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35255178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35315430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35388593	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35394420	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35495064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35656901	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36011161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36055955	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36105493	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55693063	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7019804	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71507684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71507685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71507686	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71507687	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7869547	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9696536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103190600-103224600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:103191800-103228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:103196200-103226400	Weak transcription	Psoas Muscle	Psoas
4	chr9:103207000-103227400	Weak transcription	Brain Anterior Caudate	brain
5	chr9:103208800-103227200	Weak transcription	Brain Angular Gyrus	brain
6	chr9:103208800-103227800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:103209600-103227400	Weak transcription	Brain Substantia Nigra	brain
8	chr9:103214200-103224600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:103214600-103224800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:103215200-103224600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:103215600-103227400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:103215600-103231200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:103215800-103224600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:103215800-103227400	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:103216200-103224600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:103216200-103225000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:103216600-103224600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:103216600-103228400	Weak transcription	Adipose Nuclei	Adipose
19	chr9:103216600-103235000	Weak transcription	Aorta	Aorta
20	chr9:103216800-103224800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:103216800-103225600	Weak transcription	A549	lung
22	chr9:103216800-103227400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:103216800-103227600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:103216800-103227600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:103216800-103228600	Weak transcription	Left Ventricle	heart
26	chr9:103216800-103228600	Weak transcription	Pancreas	Pancrea
27	chr9:103216800-103235000	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:103217000-103234800	Weak transcription	Fetal Brain Female	brain
29	chr9:103217200-103234800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:103217400-103227600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:103218200-103227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:103218200-103235000	Weak transcription	NHLF	lung
33	chr9:103218400-103235000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:103220200-103234800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:103223000-103224600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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