Variant report

Variant	rs12248509
Chromosome Location	chr10:95997190-95997191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11187828	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12240281	0.82[AFR][1000 genomes]
rs12249757	0.80[AMR][1000 genomes]
rs12258052	0.87[LWK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs12262808	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1408820	0.90[LWK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs1969867	0.82[AFR][1000 genomes]
rs2274225	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs34775698	0.86[AFR][1000 genomes]
rs4917450	0.93[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4918172	0.88[AFR][1000 genomes]
rs4918182	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs4918184	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs7072099	0.82[AFR][1000 genomes]
rs7081879	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs7083628	0.83[AFR][1000 genomes]
rs7919066	0.96[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7919320	0.93[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9663810	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9787457	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9787670	0.88[AFR][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	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription 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 target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12248509	SF3B1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95970800-96005800	Weak transcription	Colonic Mucosa	Colon
2	chr10:95973400-96012200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:95974200-96034000	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:95984600-96000600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:95984800-96023800	Weak transcription	Pancreas	Pancrea
6	chr10:95985800-96005800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:95985800-96033800	Weak transcription	Left Ventricle	heart
8	chr10:95986000-96011400	Weak transcription	Stomach Mucosa	stomach
9	chr10:95987000-95998600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:95988000-95997400	Weak transcription	Aorta	Aorta
11	chr10:95988200-96005600	Weak transcription	Fetal Brain Female	brain
12	chr10:95989400-96005800	Weak transcription	Ovary	ovary
13	chr10:95989400-96005800	Weak transcription	Spleen	Spleen
14	chr10:95990000-95997400	Strong transcription	Fetal Muscle Leg	muscle
15	chr10:95992800-95997600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:95994200-95997200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr10:95994400-95997400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr10:95994600-96005800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr10:95994600-96045400	Weak transcription	Lung	lung
20	chr10:95994800-96005800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr10:95995000-95997200	Weak transcription	Fetal Stomach	stomach
22	chr10:95995000-96005800	Weak transcription	Gastric	stomach
23	chr10:95995200-95997400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr10:95995200-96005800	Weak transcription	HSMMtube	muscle
25	chr10:95995800-95997400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr10:95995800-95997800	Enhancers	Fetal Lung	lung
27	chr10:95995800-95999600	Weak transcription	Small Intestine	intestine
28	chr10:95995800-96005800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:95995800-96005800	Weak transcription	Adipose Nuclei	Adipose
30	chr10:95995800-96051800	Weak transcription	Fetal Kidney	kidney
31	chr10:95996000-95997200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr10:95996000-95997400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:95996000-96002000	Weak transcription	Fetal Intestine Small	intestine
34	chr10:95996000-96005600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:95996200-95997200	Weak transcription	A549	lung
36	chr10:95996200-95997400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr10:95996200-95998400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:95996600-95997600	Weak transcription	Fetal Intestine Large	intestine
39	chr10:95996800-95997800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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