Variant report

Variant	rs997694
Chromosome Location	chr9:16484870-16484871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs34006539	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS 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	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv892646	chr9:16476144-16514375	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS	lncRNA	n/a	inside rSNPs	diseases
6	nsv892647	chr9:16476144-16521534	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv466265	chr9:16484731-16516941	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
8	nsv613670	chr9:16484731-16516941	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs997694	BNC2	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16457800-16493400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:16459600-16499800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:16459600-16500000	Weak transcription	NHLF	lung
4	chr9:16460800-16485400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:16471000-16504600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:16482400-16488600	Enhancers	Colon Smooth Muscle	Colon
7	chr9:16483000-16485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:16483200-16485000	Enhancers	Stomach Smooth Muscle	stomach
9	chr9:16483200-16513600	Weak transcription	Psoas Muscle	Psoas
10	chr9:16483600-16485200	Enhancers	Fetal Lung	lung
11	chr9:16483600-16485600	Enhancers	Fetal Kidney	kidney
12	chr9:16483600-16491400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:16483800-16490400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr9:16484000-16485400	Enhancers	Rectal Smooth Muscle	rectum
15	chr9:16484000-16485800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:16484000-16485800	Enhancers	Ovary	ovary
17	chr9:16484000-16486600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:16484000-16490000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr9:16484200-16486200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:16484200-16486200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:16484200-16488200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr9:16484400-16485000	Enhancers	HSMM	muscle
23	chr9:16484400-16485400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr9:16484400-16485800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr9:16484400-16486800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:16484400-16489400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr9:16484600-16485200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:16484600-16485400	Enhancers	HMEC	breast
29	chr9:16484600-16485400	Enhancers	HSMMtube	muscle
30	chr9:16484600-16485400	Enhancers	Osteobl	bone
31	chr9:16484600-16485800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr9:16484600-16487600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:16484800-16485000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:16484800-16485800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr9:16484800-16485800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr9:16484800-16486000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:16484800-16487600	Weak transcription	Fetal Stomach	stomach

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