Variant report

Variant	rs12349968
Chromosome Location	chr9:71396426-71396427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71339890..71342700-chr9:71395822..71397437,2	K562	blood:
2	chr9:71392687..71396802-chr9:71403243..71407898,5	MCF-7	breast:
3	chr9:71395139..71397780-chr9:71401800..71403329,2	MCF-7	breast:
4	chr9:71357154..71359879-chr9:71394031..71396553,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107242	Chromatin interaction
ENSG00000236998	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11143619	0.83[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11143645	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11143693	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12000106	0.88[YRI][hapmap]
rs12005775	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12006032	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12342394	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2151414	1.00[ASW][hapmap];0.85[CEU][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7030788	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs950785	0.80[AMR][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	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71394000-71396600	Active TSS	K562	blood
2	chr9:71394200-71396800	Active TSS	Psoas Muscle	Psoas
3	chr9:71394600-71396800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:71394600-71396800	Active TSS	Right Ventricle	heart
5	chr9:71394800-71396800	Active TSS	NHLF	lung
6	chr9:71395200-71397800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:71395400-71396800	Active TSS	Right Atrium	heart
8	chr9:71395400-71397200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr9:71395600-71396600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:71395600-71400200	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr9:71395800-71396600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:71395800-71396800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:71395800-71397000	Weak transcription	Gastric	stomach
14	chr9:71395800-71398800	Enhancers	Small Intestine	intestine
15	chr9:71395800-71400200	Enhancers	Primary B cells from peripheral blood	blood
16	chr9:71396000-71396600	Active TSS	Fetal Intestine Small	intestine
17	chr9:71396000-71396800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:71396000-71396800	Weak transcription	Esophagus	oesophagus
19	chr9:71396000-71396800	Weak transcription	Placenta	Placenta
20	chr9:71396000-71396800	Weak transcription	Lung	lung
21	chr9:71396000-71396800	Weak transcription	Pancreas	Pancrea
22	chr9:71396000-71396800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:71396000-71397000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:71396000-71397000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:71396000-71397000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr9:71396000-71397200	Flanking Active TSS	GM12878-XiMat	blood
27	chr9:71396000-71397400	Enhancers	Primary B cells from cord blood	blood
28	chr9:71396000-71397800	Enhancers	Brain Substantia Nigra	brain
29	chr9:71396000-71398000	Enhancers	Stomach Mucosa	stomach
30	chr9:71396000-71398600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr9:71396000-71399000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr9:71396000-71399000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr9:71396000-71399200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:71396000-71400400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr9:71396000-71402400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:71396000-71403400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr9:71396000-71408200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:71396200-71396600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr9:71396200-71396600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:71396200-71396600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:71396200-71396600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:71396200-71396600	Active TSS	Fetal Lung	lung
43	chr9:71396200-71396600	Weak transcription	Left Ventricle	heart
44	chr9:71396200-71396600	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr9:71396200-71396600	Weak transcription	Thymus	Thymus
46	chr9:71396200-71396800	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr9:71396200-71396800	Enhancers	Primary T cells from cord blood	blood
48	chr9:71396200-71396800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr9:71396200-71396800	Enhancers	Adipose Nuclei	Adipose
50	chr9:71396200-71396800	Weak transcription	Aorta	Aorta

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