Variant report

Variant	rs12338480
Chromosome Location	chr9:108178794-108178795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108176485..108179164-chr9:108369802..108371532,2	K562	blood:
2	chr9:108006433..108008412-chr9:108176076..108179164,3	MCF-7	breast:
3	chr9:108005319..108006844-chr9:108176651..108179101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070214	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10115811	0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10115838	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10119410	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10119483	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10121304	0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10123783	0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10125150	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10125368	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441742	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441743	0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441771	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441772	0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441773	0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441774	0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12004028	0.83[AMR][1000 genomes]
rs12336341	0.83[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12337845	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12340242	0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12346497	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12348967	0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12349041	0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12349068	0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12353548	0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28456113	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28461171	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28541347	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28613030	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56965223	0.83[AMR][1000 genomes]
rs57430142	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57497195	0.83[AMR][1000 genomes]
rs7028140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7028216	0.85[AMR][1000 genomes]
rs9299388	0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108175400-108179400	Enhancers	Liver	Liver
2	chr9:108175600-108181200	Enhancers	HepG2	liver
3	chr9:108175800-108181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:108176200-108181000	Weak transcription	Adipose Nuclei	Adipose
5	chr9:108176200-108188200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:108176400-108180800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:108177600-108186400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:108177800-108178800	Weak transcription	GM12878-XiMat	blood
9	chr9:108177800-108179200	Weak transcription	Fetal Brain Male	brain
10	chr9:108177800-108179400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:108177800-108179400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr9:108177800-108180800	Weak transcription	Fetal Lung	lung
13	chr9:108177800-108180800	Weak transcription	Stomach Mucosa	stomach
14	chr9:108177800-108181000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr9:108177800-108181000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:108177800-108181000	Weak transcription	A549	lung
17	chr9:108177800-108182200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:108177800-108194200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:108177800-108194200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr9:108178000-108179000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:108178000-108179400	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:108178000-108180800	Weak transcription	Brain Angular Gyrus	brain
23	chr9:108178000-108181000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr9:108178000-108181800	Weak transcription	Fetal Intestine Small	intestine
25	chr9:108178200-108179200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:108178200-108180600	Weak transcription	Fetal Intestine Large	intestine
27	chr9:108178200-108181000	Weak transcription	Brain Anterior Caudate	brain
28	chr9:108178400-108179200	Weak transcription	Brain Substantia Nigra	brain

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