Variant report

Variant	rs73656558
Chromosome Location	chr9:98570226-98570227
allele	C/G
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:
2	chr9:98540410..98542743-chr9:98568688..98571195,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTCH1-3	chr9:98568370-98576204	NONHSAT133392
2	lnc-PTCH1-3	chr9:98568376-98570719	NONHSAT133393

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs55747426	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56002461	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73656566	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73656583	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7859542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7874318	0.89[AFR][1000 genomes];1.00[AMR][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:47 , 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	chr9:98567400-98570800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:98568000-98571400	Enhancers	Ovary	ovary
5	chr9:98568600-98570600	Enhancers	Colon Smooth Muscle	Colon
6	chr9:98568600-98570600	Enhancers	Fetal Stomach	stomach
7	chr9:98568600-98571200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr9:98568800-98570600	Enhancers	NHLF	lung
9	chr9:98568800-98573800	Weak transcription	Brain Substantia Nigra	brain
10	chr9:98569000-98570400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:98569000-98570400	Enhancers	Left Ventricle	heart
12	chr9:98569000-98570600	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr9:98569200-98570400	Enhancers	Rectal Smooth Muscle	rectum
14	chr9:98569400-98570800	Enhancers	HUVEC	blood vessel
15	chr9:98569600-98570400	Enhancers	Right Ventricle	heart
16	chr9:98569600-98570400	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr9:98569600-98570400	Flanking Active TSS	HepG2	liver
18	chr9:98569600-98570600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:98569600-98570600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:98569600-98570600	Enhancers	Liver	Liver
21	chr9:98569600-98570600	Flanking Active TSS	GM12878-XiMat	blood
22	chr9:98569600-98571000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:98569600-98571000	Enhancers	Fetal Lung	lung
24	chr9:98569800-98571000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:98569800-98575800	Weak transcription	Aorta	Aorta
26	chr9:98569800-98576200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr9:98570000-98570600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:98570000-98571000	Enhancers	Brain Hippocampus Middle	brain
29	chr9:98570000-98575400	Weak transcription	Fetal Kidney	kidney
30	chr9:98570200-98570400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:98570200-98570400	Enhancers	Brain Anterior Caudate	brain
32	chr9:98570200-98570400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr9:98570200-98570400	Enhancers	Fetal Intestine Small	intestine
34	chr9:98570200-98570400	Enhancers	Fetal Muscle Trunk	muscle
35	chr9:98570200-98570400	Enhancers	Gastric	stomach
36	chr9:98570200-98570400	Enhancers	Right Atrium	heart
37	chr9:98570200-98570400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr9:98570200-98570400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr9:98570200-98570600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr9:98570200-98570600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:98570200-98570600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:98570200-98570600	Enhancers	Duodenum Mucosa	Duodenum
43	chr9:98570200-98570600	Enhancers	Fetal Muscle Leg	muscle
44	chr9:98570200-98570600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr9:98570200-98570800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr9:98570200-98571000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:98570200-98571000	Enhancers	Placenta Amnion	Placenta Amnion

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