Variant report

Variant	rs1337399
Chromosome Location	chr9:16708146-16708147
allele	A/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	GATA3	chr9:16708104-16708316	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
BNC2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10511624	0.89[CEU][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10511625	0.94[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10733313	0.95[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10733314	0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10733315	0.90[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10733316	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10738445	0.84[CEU][hapmap]
rs10738446	0.84[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10738447	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10738448	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10738449	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756781	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10756782	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10756783	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10756784	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10756785	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10756786	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10756787	0.90[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810591	0.95[CEU][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10810592	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810593	0.89[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10962542	0.89[CEU][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10962546	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1888207	0.89[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1888208	0.90[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2297174	0.95[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297176	0.89[CEU][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2383004	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3850444	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs3850445	1.00[CEU][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3861709	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3904778	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs4111334	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4111335	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4360380	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4961732	0.90[CEU][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs4961733	0.81[EUR][1000 genomes]
rs4961734	0.90[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4961735	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4961736	0.94[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6651521	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7028900	0.90[CEU][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.87[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:64 , 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	chr9:16705600-16708200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:16705600-16708400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:16705600-16708400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:16705600-16708400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:16705600-16708400	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:16705600-16708400	Weak transcription	Gastric	stomach
13	chr9:16705600-16708400	Weak transcription	Ovary	ovary
14	chr9:16705600-16708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:16705600-16708600	Weak transcription	Placenta	Placenta
16	chr9:16705600-16708800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:16705600-16708800	Weak transcription	Lung	lung
18	chr9:16705600-16713800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:16705800-16708200	Weak transcription	NHEK	skin
20	chr9:16705800-16708400	Weak transcription	Fetal Stomach	stomach
21	chr9:16705800-16708600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:16705800-16708600	Weak transcription	Fetal Brain Female	brain
23	chr9:16705800-16709000	Weak transcription	Adipose Nuclei	Adipose
24	chr9:16706000-16708600	Weak transcription	Fetal Kidney	kidney
25	chr9:16706400-16708400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:16706400-16708400	Weak transcription	HSMMtube	muscle
27	chr9:16706600-16708400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:16706600-16708400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:16706600-16708400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:16706600-16708400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:16706600-16708400	Weak transcription	HSMM	muscle
32	chr9:16706600-16708600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr9:16706600-16709000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:16706600-16711000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:16706800-16708200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:16706800-16708200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:16706800-16708200	Weak transcription	Hela-S3	cervix
38	chr9:16706800-16708400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:16706800-16708400	Weak transcription	NH-A	brain
40	chr9:16706800-16708400	Weak transcription	NHDF-Ad	bronchial
41	chr9:16706800-16708400	Weak transcription	NHLF	lung
42	chr9:16706800-16708400	Weak transcription	Osteobl	bone
43	chr9:16707000-16708200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:16707000-16708200	Weak transcription	A549	lung
45	chr9:16707000-16708400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:16707000-16708400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr9:16707200-16708800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:16707400-16712000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr9:16707600-16708200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr9:16707600-16708400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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