Variant report

Variant	rs12004019
Chromosome Location	chr9:108247951-108247952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108241533..108244376-chr9:108246766..108248301,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10991682	0.87[AFR][1000 genomes]
rs11999966	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12002748	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12004886	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12342071	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13362922	0.85[AFR][1000 genomes]
rs1808155	0.86[AFR][1000 genomes]
rs1854124	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2149592	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2149593	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2417627	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41277781	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66820447	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7033452	0.90[AFR][1000 genomes]
rs7034699	0.88[AFR][1000 genomes]
rs7034702	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042000	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7858616	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7867012	0.89[AFR][1000 genomes]
rs7870485	0.90[AFR][1000 genomes]
rs9657645	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108211000-108248000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
3	chr9:108220400-108252600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:108221000-108257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:108221000-108257200	Weak transcription	Fetal Stomach	stomach
6	chr9:108221000-108266000	Weak transcription	NHEK	skin
7	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
8	chr9:108222200-108259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:108222200-108277000	Weak transcription	Ovary	ovary
10	chr9:108222400-108259000	Weak transcription	HSMMtube	muscle
11	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
12	chr9:108223200-108252600	Weak transcription	K562	blood
13	chr9:108223600-108255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:108225000-108249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:108227400-108271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:108228000-108258800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr9:108228200-108250200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:108228400-108252400	Weak transcription	Fetal Intestine Large	intestine
20	chr9:108228400-108257600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:108231400-108250200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr9:108231400-108257000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:108231600-108249800	Weak transcription	NHLF	lung
24	chr9:108231800-108254400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:108232000-108252200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:108232400-108248400	Weak transcription	Primary B cells from cord blood	blood
28	chr9:108232400-108249400	Weak transcription	HMEC	breast
29	chr9:108232400-108249800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:108232600-108268800	Weak transcription	Fetal Brain Female	brain
31	chr9:108233000-108255000	Weak transcription	Dnd41	blood
32	chr9:108233400-108253000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:108233400-108253000	Weak transcription	Hela-S3	cervix
34	chr9:108233600-108250200	Weak transcription	A549	lung
35	chr9:108233600-108250400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:108233600-108269200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:108233600-108272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:108233600-108272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:108233600-108277000	Weak transcription	Adipose Nuclei	Adipose
40	chr9:108233800-108249600	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:108235400-108250200	Weak transcription	HSMM	muscle
42	chr9:108235800-108249000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:108236400-108259000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:108237800-108250200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:108237800-108259200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:108238800-108250000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:108239000-108253800	Weak transcription	NHDF-Ad	bronchial
48	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
49	chr9:108243400-108250600	Weak transcription	Brain Hippocampus Middle	brain
50	chr9:108243400-108250600	Weak transcription	Brain Inferior Temporal Lobe	brain

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