Variant report

Variant	rs11187825
Chromosome Location	chr10:95987313-95987314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr10:95987281-95987455	H1-hESC	embryonic stem cell:	n/a	chr10:95987349-95987363 chr10:95987361-95987370

Variant related genes	Relation type
ENSG00000228553	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10882405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10882407	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882409	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11187832	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1547643	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2860749	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860750	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3980310	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4113810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4388804	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4477375	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7069316	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7085875	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7098833	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910752	0.84[CEU][hapmap]
rs7914268	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs816278	0.81[CEU][hapmap]
rs9325467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9419788	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs9663515	0.88[AMR][1000 genomes];0.89[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11187825	CYP2C19	cis	cerebellum	SCAN
rs11187825	HELLS	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95960000-95991800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr10:95967400-95988000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr10:95970800-96005800	Weak transcription	Colonic Mucosa	Colon
4	chr10:95971000-95994000	Weak transcription	Gastric	stomach
5	chr10:95973400-96012200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:95974200-96034000	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:95974400-95987800	Weak transcription	Fetal Brain Female	brain
8	chr10:95975200-95992600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:95980600-95993800	Weak transcription	HSMMtube	muscle
10	chr10:95981000-95987400	Weak transcription	Fetal Intestine Large	intestine
11	chr10:95982400-95989200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr10:95982800-95992400	Weak transcription	Lung	lung
13	chr10:95983200-95993800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr10:95983400-95991400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr10:95984600-95995800	Weak transcription	Fetal Lung	lung
16	chr10:95984600-96000600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr10:95984800-95988200	Weak transcription	Ovary	ovary
18	chr10:95984800-96023800	Weak transcription	Pancreas	Pancrea
19	chr10:95985000-95994800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr10:95985000-95995000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:95985600-95995000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr10:95985800-95989000	Weak transcription	A549	lung
23	chr10:95985800-96005800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:95985800-96033800	Weak transcription	Left Ventricle	heart
25	chr10:95986000-95987800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:95986000-95994800	Weak transcription	Adipose Nuclei	Adipose
27	chr10:95986000-96011400	Weak transcription	Stomach Mucosa	stomach
28	chr10:95987000-95988000	Strong transcription	Aorta	Aorta
29	chr10:95987000-95988000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr10:95987000-95988200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr10:95987000-95990400	Strong transcription	Fetal Intestine Small	intestine
32	chr10:95987000-95993800	Weak transcription	Fetal Brain Male	brain
33	chr10:95987000-95995000	Strong transcription	Fetal Stomach	stomach
34	chr10:95987000-95998600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr10:95987200-95988400	Strong transcription	Fetal Muscle Leg	muscle
36	chr10:95987200-95989200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr10:95987200-95989600	Strong transcription	Fetal Muscle Trunk	muscle

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