Variant report

Variant	rs11169768
Chromosome Location	chr12:39233038-39233039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10161183	0.94[ASN][1000 genomes]
rs10444553	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs10876208	0.86[ASN][1000 genomes]
rs11169482	0.90[JPT][hapmap]
rs11169508	1.00[YRI][hapmap]
rs11169518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11169519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11169535	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11169616	0.95[ASN][1000 genomes]
rs11169760	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11169807	0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs1400280	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1400285	0.88[ASN][1000 genomes]
rs1403521	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1516558	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs1523118	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1523121	0.99[ASN][1000 genomes]
rs1586373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2388172	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs34246358	0.96[ASN][1000 genomes]
rs35749392	0.92[ASN][1000 genomes]
rs3803020	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3887436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4384412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4595586	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768388	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56149694	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56344858	0.97[ASN][1000 genomes]
rs6580849	1.00[JPT][hapmap]
rs7314227	0.92[ASN][1000 genomes]
rs7315271	0.90[JPT][hapmap]
rs7957376	0.90[JPT][hapmap]
rs7957999	0.82[ASN][1000 genomes]
rs7962363	1.00[JPT][hapmap];0.83[TSI][hapmap]
rs7970097	1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap]

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	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11169768	SYT10	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39203200-39276000	Weak transcription	Aorta	Aorta
2	chr12:39204000-39284800	Weak transcription	Lung	lung
3	chr12:39206600-39243800	Weak transcription	Left Ventricle	heart
4	chr12:39206600-39249200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:39206800-39241400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:39206800-39241400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:39216000-39237400	Weak transcription	Hela-S3	cervix
8	chr12:39219200-39242600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:39221800-39251800	Weak transcription	Liver	Liver
10	chr12:39223600-39238400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:39224000-39241800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:39227800-39237200	Weak transcription	GM12878-XiMat	blood
13	chr12:39229400-39252200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:39231800-39233200	Enhancers	Fetal Intestine Large	intestine
15	chr12:39231800-39233200	Enhancers	Fetal Intestine Small	intestine
16	chr12:39232000-39233200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:39232200-39239200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:39232400-39247600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:39232600-39233200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:39232800-39233200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr12:39232800-39233200	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr12:39233000-39233200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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