Variant report

Variant	rs892647
Chromosome Location	chr9:98571239-98571240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98569719..98571881-chr9:98585000..98587559,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTCH1-3	chr9:98568370-98576204	NONHSAT133392

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11998816	1.00[EUR][1000 genomes]
rs12000947	1.00[EUR][1000 genomes]
rs12001253	1.00[EUR][1000 genomes]
rs12004258	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12004510	1.00[EUR][1000 genomes]
rs12004765	1.00[EUR][1000 genomes]
rs3991704	0.93[AFR][1000 genomes]
rs45604033	1.00[EUR][1000 genomes]
rs4742769	0.89[AFR][1000 genomes]
rs55870020	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56275194	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56938111	1.00[EUR][1000 genomes]
rs58715455	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59046245	0.97[AFR][1000 genomes]
rs59510923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60301271	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6478983	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479043	1.00[EUR][1000 genomes]
rs7021641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7030427	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031397	0.95[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7047126	0.95[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73656543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73656554	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73656561	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73656564	0.99[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7875882	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:33 , 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	chr9:98568000-98571400	Enhancers	Ovary	ovary
4	chr9:98568800-98573800	Weak transcription	Brain Substantia Nigra	brain
5	chr9:98569800-98575800	Weak transcription	Aorta	Aorta
6	chr9:98569800-98576200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:98570000-98575400	Weak transcription	Fetal Kidney	kidney
8	chr9:98570400-98574000	Enhancers	Stomach Smooth Muscle	stomach
9	chr9:98570400-98575800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:98570400-98577400	Weak transcription	Brain Anterior Caudate	brain
11	chr9:98570400-98577600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:98570400-98577600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:98570400-98577600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:98570400-98580800	Weak transcription	Fetal Intestine Small	intestine
15	chr9:98570400-98585800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:98570400-98589200	Weak transcription	Left Ventricle	heart
17	chr9:98570400-98589200	Weak transcription	Right Ventricle	heart
18	chr9:98570400-98593200	Weak transcription	Gastric	stomach
19	chr9:98570400-98593800	Weak transcription	Right Atrium	heart
20	chr9:98570600-98572000	Enhancers	GM12878-XiMat	blood
21	chr9:98570600-98573400	Weak transcription	Fetal Stomach	stomach
22	chr9:98570600-98573600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:98570600-98576000	Weak transcription	NHLF	lung
24	chr9:98570600-98579200	Weak transcription	Liver	Liver
25	chr9:98570600-98579600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:98570600-98585000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:98570800-98576600	Weak transcription	HUVEC	blood vessel
28	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:98571000-98573000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr9:98571000-98574200	Weak transcription	Fetal Lung	lung
31	chr9:98571000-98575200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:98571000-98582000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:98571200-98577200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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