Variant report

Variant	rs12275068
Chromosome Location	chr11:17546856-17546857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12270598	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12273896	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16934376	0.85[JPT][hapmap]
rs2355021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41282940	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4756899	0.87[YRI][hapmap]
rs7112757	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72870321	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72870323	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72870330	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs733126	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs878545	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs886817	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv33415	chr11:17532596-17549436	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv934119	chr11:17542691-17548601	Weak transcription Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12275068	SOX6	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
2	chr11:17527600-17549200	Strong transcription	Duodenum Mucosa	Duodenum
3	chr11:17529800-17548600	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr11:17531600-17547200	Strong transcription	Fetal Intestine Large	intestine
5	chr11:17531800-17552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:17532200-17547200	Strong transcription	Fetal Intestine Small	intestine
7	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
8	chr11:17539600-17550000	Weak transcription	Spleen	Spleen
9	chr11:17540800-17552400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:17541000-17552600	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr11:17541400-17548000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:17541400-17552400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:17541600-17549600	Weak transcription	Brain Anterior Caudate	brain
14	chr11:17541600-17550000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:17541600-17551600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:17541600-17555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:17542000-17547800	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:17542000-17548000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:17542400-17547800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:17542600-17549400	Weak transcription	Brain Angular Gyrus	brain
21	chr11:17542600-17550000	Weak transcription	Brain Substantia Nigra	brain
22	chr11:17544000-17549800	Strong transcription	Colonic Mucosa	Colon
23	chr11:17544200-17548000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:17545200-17547400	Weak transcription	Fetal Stomach	stomach
25	chr11:17545400-17553000	Weak transcription	Gastric	stomach
26	chr11:17545800-17550000	Weak transcription	Right Atrium	heart
27	chr11:17546800-17550000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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