Variant report

Variant	rs16929764
Chromosome Location	chr9:12880600-12880601
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	TCF7L2	chr9:12880237-12880927	HEK293	kidney:	n/a	n/a
2	KAP1	chr9:12880424-12881092	HEK293	kidney:	n/a	n/a
3	GATA3	chr9:12880511-12881082	SH-SY5Y	brain:	n/a	n/a
4	KAP1	chr9:12880105-12881193	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12817203..12820022-chr9:12879979..12881998,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222658	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12344174	0.93[EUR][1000 genomes]
rs13284880	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13286083	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13295684	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13297021	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13299801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13300480	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13301620	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1412308	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16929768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16929788	0.93[EUR][1000 genomes]
rs1831561	0.93[EUR][1000 genomes]
rs34040994	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34086294	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34297034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34660175	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35253144	0.82[EUR][1000 genomes]
rs35313919	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35685701	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35696782	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35858006	0.93[EUR][1000 genomes]
rs36050768	0.80[EUR][1000 genomes]
rs36080084	0.93[EUR][1000 genomes]
rs36196009	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71507337	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71507342	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv613615	chr9:12830070-12947238	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12875200-12884800	Weak transcription	HMEC	breast
2	chr9:12875800-12880600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:12876800-12881600	Enhancers	Hela-S3	cervix
4	chr9:12877400-12882000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:12877600-12882200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:12878000-12880600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:12878000-12883000	Enhancers	A549	lung
8	chr9:12878400-12880600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:12879000-12880800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:12879000-12882200	Weak transcription	NH-A	brain
11	chr9:12879000-12884800	Weak transcription	Liver	Liver
12	chr9:12879000-12884800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr9:12879200-12881800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr9:12879600-12880600	Weak transcription	Small Intestine	intestine
15	chr9:12879800-12881200	Enhancers	Fetal Intestine Small	intestine
16	chr9:12880000-12881200	Enhancers	Colon Smooth Muscle	Colon
17	chr9:12880000-12881200	Enhancers	Rectal Smooth Muscle	rectum
18	chr9:12880000-12883800	Enhancers	NHLF	lung
19	chr9:12880000-12884200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:12880200-12881000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr9:12880200-12883800	Enhancers	NHDF-Ad	bronchial
22	chr9:12880400-12880600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr9:12880400-12880800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:12880400-12880800	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr9:12880400-12881000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:12880400-12881000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:12880400-12881000	Enhancers	Fetal Intestine Large	intestine
28	chr9:12880400-12881000	Enhancers	Fetal Kidney	kidney
29	chr9:12880400-12881200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr9:12880400-12881200	Enhancers	NHEK	skin
31	chr9:12880400-12881400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:12880400-12881400	Enhancers	Fetal Stomach	stomach
33	chr9:12880400-12881600	Enhancers	Fetal Lung	lung
34	chr9:12880400-12881600	Enhancers	Stomach Mucosa	stomach
35	chr9:12880400-12884000	Enhancers	Osteobl	bone
36	chr9:12880600-12880800	Enhancers	Adipose Nuclei	Adipose
37	chr9:12880600-12880800	Enhancers	Small Intestine	intestine
38	chr9:12880600-12881000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:12880600-12881000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr9:12880600-12881000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr9:12880600-12881000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:12880600-12881000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:12880600-12881000	Enhancers	Fetal Muscle Leg	muscle
44	chr9:12880600-12881200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr9:12880600-12881200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr9:12880600-12881200	Enhancers	Rectal Mucosa Donor 29	rectum

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