Variant report

Variant	rs7030427
Chromosome Location	chr9:98576055-98576056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTCH1-3	chr9:98575575-98576204	ENSG00000175611
2	lnc-PTCH1-3	chr9:98568370-98576204	NONHSAT133392
3	lnc-C9orf102-7	chr9:98575836-98576850	NONHSAT133395

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10760261	0.87[YRI][hapmap]
rs10760269	0.87[YRI][hapmap]
rs10985499	0.86[YRI][hapmap]
rs11998816	1.00[EUR][1000 genomes]
rs12000947	1.00[EUR][1000 genomes]
rs12001253	1.00[EUR][1000 genomes]
rs12004258	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12004510	1.00[EUR][1000 genomes]
rs12004765	1.00[EUR][1000 genomes]
rs3991704	0.94[AFR][1000 genomes]
rs45604033	1.00[EUR][1000 genomes]
rs4742769	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs55870020	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56275194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56938111	1.00[EUR][1000 genomes]
rs58715455	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59046245	0.95[AFR][1000 genomes]
rs59510923	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60301271	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6478983	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479043	1.00[EUR][1000 genomes]
rs7021641	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031397	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7039115	1.00[EUR][1000 genomes]
rs7041571	1.00[EUR][1000 genomes]
rs7043426	1.00[EUR][1000 genomes]
rs7043732	1.00[EUR][1000 genomes]
rs7046189	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7047126	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73528896	1.00[EUR][1000 genomes]
rs73528901	1.00[EUR][1000 genomes]
rs73530711	1.00[EUR][1000 genomes]
rs73534614	1.00[EUR][1000 genomes]
rs73656542	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73656543	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73656554	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73656561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73656564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7847478	1.00[EUR][1000 genomes]
rs7850319	1.00[EUR][1000 genomes]
rs7854738	1.00[EUR][1000 genomes]
rs7860019	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7875882	1.00[EUR][1000 genomes]
rs892647	0.99[AFR][1000 genomes];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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98548400-98578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:98557400-98577200	Weak transcription	Pancreas	Pancrea
3	chr9:98569800-98576200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:98570400-98577400	Weak transcription	Brain Anterior Caudate	brain
5	chr9:98570400-98577600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:98570400-98577600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:98570400-98577600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr9:98570400-98580800	Weak transcription	Fetal Intestine Small	intestine
9	chr9:98570400-98585800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:98570400-98589200	Weak transcription	Left Ventricle	heart
11	chr9:98570400-98589200	Weak transcription	Right Ventricle	heart
12	chr9:98570400-98593200	Weak transcription	Gastric	stomach
13	chr9:98570400-98593800	Weak transcription	Right Atrium	heart
14	chr9:98570600-98579200	Weak transcription	Liver	Liver
15	chr9:98570600-98579600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:98570600-98585000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:98570800-98576600	Weak transcription	HUVEC	blood vessel
18	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:98571000-98582000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:98571200-98577200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr9:98572400-98579000	Weak transcription	Primary T cells from cord blood	blood
22	chr9:98572800-98582400	Weak transcription	Brain Germinal Matrix	brain
23	chr9:98573000-98585400	Weak transcription	Thymus	Thymus
24	chr9:98573600-98576200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr9:98573800-98577200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:98574000-98576200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:98574000-98576400	Weak transcription	Brain Angular Gyrus	brain
28	chr9:98574200-98576200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:98574200-98576400	Weak transcription	Brain Substantia Nigra	brain
30	chr9:98574600-98577600	Weak transcription	Fetal Stomach	stomach
31	chr9:98575800-98576400	Weak transcription	Fetal Lung	lung
32	chr9:98575800-98579600	Enhancers	HSMM	muscle
33	chr9:98575800-98579800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:98576000-98576600	Enhancers	NHLF	lung
35	chr9:98576000-98577200	Enhancers	Fetal Heart	heart
36	chr9:98576000-98577400	Enhancers	Ovary	ovary
37	chr9:98576000-98579200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:98576000-98579800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:98576000-98579800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr9:98576000-98580000	Enhancers	A549	lung
41	chr9:98576000-98596000	Weak transcription	Aorta	Aorta

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