Variant report

Variant	rs7038172
Chromosome Location	chr9:16708269-16708270
allele	C/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	GATA3	chr9:16708104-16708316	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr9:16708254-16708313	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
BNC2	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10810588	0.81[CHB][hapmap]
rs16934924	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]
rs2297175	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56757209	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs66593595	0.82[AMR][1000 genomes]
rs72704097	0.82[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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16691000-16708400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:16705000-16708600	Weak transcription	Brain Substantia Nigra	brain
3	chr9:16705200-16708400	Weak transcription	Aorta	Aorta
4	chr9:16705200-16708600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:16705200-16710600	Weak transcription	Psoas Muscle	Psoas
6	chr9:16705400-16710600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:16705600-16708400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:16705600-16708400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:16705600-16708400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:16705600-16708400	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:16705600-16708400	Weak transcription	Gastric	stomach
12	chr9:16705600-16708400	Weak transcription	Ovary	ovary
13	chr9:16705600-16708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:16705600-16708600	Weak transcription	Placenta	Placenta
15	chr9:16705600-16708800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:16705600-16708800	Weak transcription	Lung	lung
17	chr9:16705600-16713800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:16705800-16708400	Weak transcription	Fetal Stomach	stomach
19	chr9:16705800-16708600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:16705800-16708600	Weak transcription	Fetal Brain Female	brain
21	chr9:16705800-16709000	Weak transcription	Adipose Nuclei	Adipose
22	chr9:16706000-16708600	Weak transcription	Fetal Kidney	kidney
23	chr9:16706400-16708400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:16706400-16708400	Weak transcription	HSMMtube	muscle
25	chr9:16706600-16708400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr9:16706600-16708400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:16706600-16708400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:16706600-16708400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:16706600-16708400	Weak transcription	HSMM	muscle
30	chr9:16706600-16708600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:16706600-16709000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:16706600-16711000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:16706800-16708400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:16706800-16708400	Weak transcription	NH-A	brain
35	chr9:16706800-16708400	Weak transcription	NHDF-Ad	bronchial
36	chr9:16706800-16708400	Weak transcription	NHLF	lung
37	chr9:16706800-16708400	Weak transcription	Osteobl	bone
38	chr9:16707000-16708400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:16707000-16708400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:16707200-16708800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:16707400-16712000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr9:16707600-16708400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr9:16707600-16708400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:16707800-16708400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr9:16707800-16708600	Enhancers	HUVEC	blood vessel
46	chr9:16707800-16713200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr9:16708000-16708400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:16708000-16708400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr9:16708000-16708600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr9:16708000-16709400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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