Variant report

Variant	rs7846746
Chromosome Location	chr9:16425640-16425641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf92-2	chr9:16424469-16426173	NONHSAT130288

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10511617	1.00[EUR][1000 genomes]
rs16934509	1.00[EUR][1000 genomes]
rs16934624	1.00[ASW][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16934651	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16934678	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6475051	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6475055	1.00[EUR][1000 genomes]
rs7020739	1.00[EUR][1000 genomes]
rs7021318	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7022640	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7035219	0.87[AMR][1000 genomes]
rs7040533	1.00[EUR][1000 genomes]
rs7042654	1.00[EUR][1000 genomes]
rs73413306	1.00[EUR][1000 genomes]
rs73413310	1.00[EUR][1000 genomes]
rs73645960	1.00[EUR][1000 genomes]
rs7864491	0.87[AMR][1000 genomes]
rs7867641	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7872124	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16416200-16435400	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:16418000-16435600	Weak transcription	HUVEC	blood vessel
3	chr9:16418200-16427600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:16418200-16435800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:16418800-16427400	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:16419400-16436200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:16419600-16435200	Weak transcription	Fetal Intestine Large	intestine
8	chr9:16419600-16435400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:16419600-16435400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:16419800-16432600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:16421800-16428200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:16421800-16431800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:16421800-16460400	Weak transcription	Aorta	Aorta
14	chr9:16422000-16429800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:16422000-16435400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:16422200-16426400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:16422400-16429800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:16422800-16435400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:16425000-16426200	Enhancers	HSMM	muscle
20	chr9:16425000-16427400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:16425200-16425800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:16425200-16426200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr9:16425200-16426200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:16425200-16426200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:16425200-16426200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:16425200-16426200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:16425200-16426200	Enhancers	Adipose Nuclei	Adipose
28	chr9:16425200-16426200	Enhancers	Fetal Kidney	kidney
29	chr9:16425200-16426200	Enhancers	Fetal Stomach	stomach
30	chr9:16425200-16426200	Enhancers	NHDF-Ad	bronchial
31	chr9:16425200-16427200	Enhancers	NHEK	skin
32	chr9:16425400-16425800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:16425400-16425800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:16425400-16426000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:16425400-16426000	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr9:16425400-16426000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:16425400-16426000	Flanking Active TSS	HSMMtube	muscle
38	chr9:16425400-16426200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr9:16425400-16426200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:16425400-16426200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr9:16425400-16426200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:16425400-16426200	Enhancers	Fetal Lung	lung
43	chr9:16425400-16426200	Flanking Active TSS	A549	lung
44	chr9:16425400-16426200	Enhancers	HMEC	breast
45	chr9:16425400-16427000	Enhancers	NHLF	lung
46	chr9:16425600-16425800	Enhancers	Osteobl	bone
47	chr9:16425600-16426000	Enhancers	H1 Cell Line	embryonic stem cell
48	chr9:16425600-16426000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr9:16425600-16426000	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr9:16425600-16426000	Flanking Active TSS	NH-A	brain

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