Variant report

Variant	rs11999602
Chromosome Location	chr9:16709876-16709877
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	JUND	chr9:16709829-16710322	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr9:16709866-16710416	H1-hESC	embryonic stem cell:	n/a	chr9:16710215-16710236
3	MAFK	chr9:16708354-16710526	H1-hESC	embryonic stem cell:	n/a	chr9:16708826-16708842 chr9:16708824-16708844 chr9:16708827-16708841 chr9:16708997-16709008 chr9:16709319-16709328 chr9:16708828-16708837 chr9:16708823-16708838 chr9:16708993-16709009 chr9:16709318-16709328 chr9:16708828-16708838

Variant related genes	Relation type
BNC2	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs73417989	0.85[AFR][1000 genomes];1.00[AMR][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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16705200-16710600	Weak transcription	Psoas Muscle	Psoas
2	chr9:16705400-16710600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:16705600-16713800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:16706600-16711000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:16707400-16712000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr9:16707800-16713200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:16708000-16711200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr9:16708000-16711400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:16708000-16718000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:16708200-16710000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr9:16708200-16713200	Enhancers	A549	lung
12	chr9:16708200-16716200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:16708600-16711000	Enhancers	Fetal Brain Female	brain
14	chr9:16708800-16710200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:16709000-16711000	Enhancers	Brain Germinal Matrix	brain
16	chr9:16709000-16711000	Enhancers	HUVEC	blood vessel
17	chr9:16709000-16711400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr9:16709000-16712000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:16709000-16726000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:16709200-16710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:16709200-16711000	Weak transcription	NHDF-Ad	bronchial
22	chr9:16709200-16711800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr9:16709200-16712600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:16709200-16712800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:16709200-16712800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:16709200-16713800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:16709200-16713800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:16709200-16718000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:16709400-16710200	Weak transcription	Fetal Lung	lung
30	chr9:16709400-16710400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr9:16709400-16710400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:16709400-16710400	Enhancers	NH-A	brain
33	chr9:16709400-16710600	Weak transcription	HSMMtube	muscle
34	chr9:16709400-16710800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr9:16709400-16710800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:16709400-16710800	Weak transcription	Brain Substantia Nigra	brain
37	chr9:16709400-16710800	Weak transcription	HSMM	muscle
38	chr9:16709400-16711000	Weak transcription	Fetal Muscle Leg	muscle
39	chr9:16709400-16711800	Enhancers	Fetal Brain Male	brain
40	chr9:16709400-16712600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:16709400-16712800	Weak transcription	Ovary	ovary
42	chr9:16709400-16714200	Weak transcription	Colon Smooth Muscle	Colon
43	chr9:16709400-16714400	Weak transcription	Osteobl	bone
44	chr9:16709400-16718600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:16709400-16719000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr9:16709600-16710400	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr9:16709600-16710600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr9:16709600-16710800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:16709600-16711000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:16709600-16712800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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