Variant report

Variant	rs16934924
Chromosome Location	chr9:16709074-16709075
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	MAFK	chr9:16708558-16709079	GM12878	blood:	n/a	chr9:16708826-16708842 chr9:16708824-16708844 chr9:16708827-16708841 chr9:16708997-16709008 chr9:16708828-16708837 chr9:16708823-16708838 chr9:16708993-16709009 chr9:16708828-16708838
2	KAP1	chr9:16708890-16709445	HEK293	kidney:	n/a	n/a
3	POLR2A	chr9:16708662-16709302	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr9:16708947-16709305	PFSK-1	brain:	n/a	n/a
5	MAFF	chr9:16708647-16709112	HepG2	liver:	n/a	chr9:16708827-16708841 chr9:16708821-16708839
6	SIN3AK20	chr9:16708983-16709487	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr9:16708476-16709309	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr9:16708483-16709297	H1-hESC	embryonic stem cell:	n/a	chr9:16708857-16708864
9	POLR2A	chr9:16708983-16709302	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr9:16708425-16709499	H1-hESC	embryonic stem cell:	n/a	n/a
11	ATF2	chr9:16708535-16709145	H1-hESC	embryonic stem cell:	n/a	n/a
12	BACH1	chr9:16708624-16709106	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr9:16708370-16709414	U87	brain:	n/a	n/a
14	HDAC2	chr9:16708515-16709183	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAFK	chr9:16708440-16709104	Hela-S3	cervix:	n/a	chr9:16708826-16708842 chr9:16708824-16708844 chr9:16708827-16708841 chr9:16708997-16709008 chr9:16708828-16708837 chr9:16708823-16708838 chr9:16708993-16709009 chr9:16708828-16708838
16	POLR2A	chr9:16708658-16709367	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr9:16708323-16709587	SK-N-MC	brain:	n/a	n/a
18	ATF2	chr9:16708465-16709294	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3A	chr9:16708613-16709480	H1-hESC	embryonic stem cell:	n/a	n/a
20	CHD1	chr9:16708845-16709561	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr9:16708398-16709421	H1-hESC	embryonic stem cell:	n/a	chr9:16708857-16708864
22	TBP	chr9:16708523-16709380	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTBP2	chr9:16708853-16709286	H1-hESC	embryonic stem cell:	n/a	n/a
24	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
25	ZNF143	chr9:16708365-16709200	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAFK	chr9:16708649-16709166	HepG2	liver:	n/a	chr9:16708826-16708842 chr9:16708824-16708844 chr9:16708827-16708841 chr9:16708997-16709008 chr9:16708828-16708837 chr9:16708823-16708838 chr9:16708993-16709009 chr9:16708828-16708838
27	MAFK	chr9:16708520-16709464	IMR90	lung:	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: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2297175	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56757209	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7038172	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][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:62 , 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	chr9:16708000-16709400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr9:16708000-16709400	Enhancers	Colon Smooth Muscle	Colon
9	chr9:16708000-16709400	Enhancers	Fetal Lung	lung
10	chr9:16708000-16711200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr9:16708000-16711400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:16708000-16718000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:16708200-16709400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr9:16708200-16709600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:16708200-16710000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr9:16708200-16713200	Enhancers	A549	lung
17	chr9:16708200-16716200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:16708400-16709200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:16708400-16709200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:16708400-16709200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:16708400-16709200	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:16708400-16709200	Enhancers	NHDF-Ad	bronchial
23	chr9:16708400-16709400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:16708400-16709400	Enhancers	Fetal Muscle Leg	muscle
25	chr9:16708400-16709400	Enhancers	HSMM	muscle
26	chr9:16708400-16709400	Enhancers	Osteobl	bone
27	chr9:16708400-16709600	Enhancers	Fetal Stomach	stomach
28	chr9:16708600-16709200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr9:16708600-16709200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr9:16708600-16709200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr9:16708600-16709200	Flanking Active TSS	Fetal Kidney	kidney
32	chr9:16708600-16709200	Enhancers	Placenta	Placenta
33	chr9:16708600-16709200	Flanking Active TSS	HSMMtube	muscle
34	chr9:16708600-16709400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:16708600-16709400	Enhancers	Brain Substantia Nigra	brain
36	chr9:16708600-16709600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:16708600-16711000	Enhancers	Fetal Brain Female	brain
38	chr9:16708800-16709200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:16708800-16709200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:16708800-16709200	Enhancers	Lung	lung
41	chr9:16708800-16709400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:16708800-16709400	Flanking Active TSS	NH-A	brain
43	chr9:16708800-16710200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr9:16709000-16709200	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr9:16709000-16709200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:16709000-16709200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:16709000-16709200	Enhancers	Fetal Brain Male	brain
48	chr9:16709000-16709200	Flanking Active TSS	Ovary	ovary
49	chr9:16709000-16709200	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr9:16709000-16709400	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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