Variant report

Variant	rs10962554
Chromosome Location	chr9:16729697-16729698
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:16729622-16730119	H1-neurons	neurons:	n/a	n/a
2	FOXA2	chr9:16729539-16730067	A549	lung:	n/a	n/a
3	POLR2A	chr9:16729619-16730065	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr9:16729552-16729763	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOS	chr9:16729617-16729817	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr9:16729555-16729856	MCF10A-Er-Src	breast:	n/a	n/a
7	REST	chr9:16729571-16730142	H1-neurons	neurons:	n/a	chr9:16729831-16729844

Variant related genes	Relation type
BNC2	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10481558	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10756788	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10756789	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10756790	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10756796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10756798	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10756800	0.80[AMR][1000 genomes]
rs10756801	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10810598	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10810601	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10810604	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10810611	0.83[EUR][1000 genomes]
rs10962548	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10962559	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13284478	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13296274	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1330303	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1952689	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34259118	0.80[AMR][1000 genomes]
rs35007358	0.80[AMR][1000 genomes]
rs62541515	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription 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	10 gene(s)	inside rSNPs	diseases
8	nsv892649	chr9:16677221-16761597	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16724400-16729800	Active TSS	Ovary	ovary
2	chr9:16728200-16729800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:16728200-16732600	Weak transcription	NHEK	skin
4	chr9:16728200-16744600	Weak transcription	Fetal Intestine Large	intestine
5	chr9:16728400-16729800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:16728400-16729800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:16728400-16729800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:16728400-16729800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:16728400-16729800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:16728400-16729800	Weak transcription	Psoas Muscle	Psoas
11	chr9:16728400-16730000	Weak transcription	Pancreas	Pancrea
12	chr9:16728400-16730000	Enhancers	NH-A	brain
13	chr9:16728400-16730600	Enhancers	Colon Smooth Muscle	Colon
14	chr9:16728400-16733600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:16728400-16736200	Weak transcription	HSMMtube	muscle
16	chr9:16728400-16743200	Weak transcription	Fetal Kidney	kidney
17	chr9:16728400-16744200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:16728600-16730000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr9:16728600-16730200	Enhancers	A549	lung
20	chr9:16728600-16730400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:16728600-16730600	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:16728600-16731200	Weak transcription	HSMM	muscle
23	chr9:16728600-16732400	Weak transcription	Adipose Nuclei	Adipose
24	chr9:16728600-16732600	Weak transcription	NHDF-Ad	bronchial
25	chr9:16728800-16743400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:16729000-16730400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:16729000-16731000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:16729000-16734400	Weak transcription	NHLF	lung
29	chr9:16729000-16743200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:16729200-16730000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:16729200-16730600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr9:16729400-16729800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr9:16729400-16729800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:16729400-16729800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:16729400-16730000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:16729400-16730000	Enhancers	Fetal Lung	lung
37	chr9:16729400-16730400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:16729400-16730400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:16729400-16730800	Enhancers	H9 Cell Line	embryonic stem cell
40	chr9:16729400-16744400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:16729600-16729800	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr9:16729600-16729800	Enhancers	Osteobl	bone
43	chr9:16729600-16730000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:16729600-16730000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:16729600-16730000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:16729600-16730200	Enhancers	Fetal Stomach	stomach
47	chr9:16729600-16730400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr9:16729600-16730600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr9:16729600-16730600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr9:16729600-16744200	Weak transcription	Muscle Satellite Cultured Cells	--

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