Variant report

Variant	rs3909252
Chromosome Location	chr9:96959110-96959111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96935573..96938519-chr9:96957688..96959458,2	K562	blood:
2	chr9:96933308..96934893-chr9:96957370..96959656,2	MCF-7	breast:
3	chr9:96773917..96776772-chr9:96957633..96960595,2	K562	blood:

Variant related genes	Relation type
ENSG00000199165	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10993081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993083	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1362820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4333674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9792534	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:96937200-96959400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:96939800-96960800	Weak transcription	NHDF-Ad	bronchial
4	chr9:96941400-96959400	Weak transcription	Spleen	Spleen
5	chr9:96942400-96964000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:96944400-96959400	Weak transcription	Psoas Muscle	Psoas
7	chr9:96946200-96959400	Weak transcription	Aorta	Aorta
8	chr9:96946200-96962800	Weak transcription	Gastric	stomach
9	chr9:96946200-96965000	Weak transcription	NHLF	lung
10	chr9:96946800-96965400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:96947000-96959400	Weak transcription	Left Ventricle	heart
12	chr9:96947000-96959800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:96947000-96966200	Weak transcription	Fetal Kidney	kidney
14	chr9:96947200-96959200	Weak transcription	NHEK	skin
15	chr9:96949400-96960200	Weak transcription	Placenta	Placenta
16	chr9:96954200-96959800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:96955000-96964600	Weak transcription	Ovary	ovary
18	chr9:96955400-96962200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:96955600-96959600	Weak transcription	HSMMtube	muscle
20	chr9:96955800-96962800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:96956800-96963000	Strong transcription	HSMM	muscle
22	chr9:96956800-96963400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:96957000-96963000	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr9:96957200-96959400	Weak transcription	Lung	lung
25	chr9:96957400-96961200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr9:96957600-96959200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:96957800-96959200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:96957800-96959400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:96957800-96959400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:96957800-96959400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:96957800-96961600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:96958000-96959400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:96958000-96960200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr9:96958200-96959200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:96958400-96959400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:96958400-96959400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:96958400-96959400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:96958400-96960400	Strong transcription	Osteobl	bone
39	chr9:96958400-96962600	Weak transcription	Primary T cells from cord blood	blood
40	chr9:96958400-96963000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:96958400-96963800	Weak transcription	Primary B cells from cord blood	blood
42	chr9:96958600-96959600	Weak transcription	Adipose Nuclei	Adipose
43	chr9:96958600-96959600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr9:96958600-96960200	Weak transcription	Brain Angular Gyrus	brain
45	chr9:96958600-96963400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:96958800-96960800	Weak transcription	Right Ventricle	heart
47	chr9:96959000-96959200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
48	chr9:96959000-96961400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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