Variant report

Variant	rs1411431
Chromosome Location	chr9:16728721-16728722
allele	G/T
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	chr9:16728536-16728781	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
BNC2	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10962547	0.85[EUR][1000 genomes]
rs10962549	0.84[EUR][1000 genomes]
rs10962552	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1411432	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4961494	0.81[EUR][1000 genomes]
rs4961741	0.87[AMR][1000 genomes]
rs59234174	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73646205	0.82[AFR][1000 genomes];0.80[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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16724400-16729800	Active TSS	Ovary	ovary
2	chr9:16724800-16728800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:16725200-16729400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:16726400-16729200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:16727800-16728800	Flanking Active TSS	Osteobl	bone
6	chr9:16727800-16729400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:16728000-16728800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:16728000-16729000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:16728200-16729800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:16728200-16732600	Weak transcription	NHEK	skin
11	chr9:16728200-16744600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:16728400-16728800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:16728400-16729000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr9:16728400-16729000	Active TSS	NHLF	lung
15	chr9:16728400-16729200	Enhancers	Fetal Lung	lung
16	chr9:16728400-16729400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:16728400-16729400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:16728400-16729400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:16728400-16729400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr9:16728400-16729400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
21	chr9:16728400-16729600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr9:16728400-16729600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:16728400-16729600	Weak transcription	Fetal Stomach	stomach
24	chr9:16728400-16729800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:16728400-16729800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:16728400-16729800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr9:16728400-16729800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:16728400-16729800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:16728400-16729800	Weak transcription	Psoas Muscle	Psoas
30	chr9:16728400-16730000	Weak transcription	Pancreas	Pancrea
31	chr9:16728400-16730000	Enhancers	NH-A	brain
32	chr9:16728400-16730600	Enhancers	Colon Smooth Muscle	Colon
33	chr9:16728400-16733600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:16728400-16736200	Weak transcription	HSMMtube	muscle
35	chr9:16728400-16743200	Weak transcription	Fetal Kidney	kidney
36	chr9:16728400-16744200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr9:16728600-16728800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:16728600-16728800	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr9:16728600-16729000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:16728600-16729200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr9:16728600-16729200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr9:16728600-16729600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr9:16728600-16729600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:16728600-16729600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:16728600-16730000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr9:16728600-16730200	Enhancers	A549	lung
47	chr9:16728600-16730400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:16728600-16730600	Enhancers	Rectal Smooth Muscle	rectum
49	chr9:16728600-16731200	Weak transcription	HSMM	muscle
50	chr9:16728600-16732400	Weak transcription	Adipose Nuclei	Adipose

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