Variant report

Variant	rs11829731
Chromosome Location	chr12:29735589-29735590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10492311	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11050323	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs11829994	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11834102	0.88[EUR][1000 genomes]
rs11834291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837554	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12310251	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12424239	0.83[EUR][1000 genomes]
rs12822100	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12826893	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12826911	0.89[CHB][hapmap]
rs12828728	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs142565	0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes]
rs148897	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs159684	1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs159688	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs159691	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs159692	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs159693	0.97[EUR][1000 genomes]
rs16934418	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs16934448	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16934474	0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16934523	1.00[CHB][hapmap]
rs16934537	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs16934556	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16934564	1.00[CHB][hapmap]
rs16934569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16934597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16934635	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2288228	0.81[CEU][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs299474	0.86[EUR][1000 genomes]
rs299477	0.91[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap]
rs299478	0.91[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs299480	0.93[EUR][1000 genomes]
rs299482	1.00[CHB][hapmap]
rs299483	1.00[CHB][hapmap]
rs299484	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs299485	0.91[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs34318689	0.83[EUR][1000 genomes]
rs55793838	0.91[AMR][1000 genomes]
rs55970961	0.91[AMR][1000 genomes]
rs56178040	0.86[ASN][1000 genomes]
rs56255721	0.91[AMR][1000 genomes]
rs56367916	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56398900	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57816450	0.91[AMR][1000 genomes]
rs58290227	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59519970	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59915017	0.91[AMR][1000 genomes]
rs67491988	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7301943	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73069592	0.91[AMR][1000 genomes]
rs73069593	0.91[AMR][1000 genomes]
rs73069598	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73071505	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73071510	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73071517	0.85[EUR][1000 genomes]
rs73071519	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73071533	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73071556	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73071582	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7315541	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74078415	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11829731	SYT10	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29709800-29756200	Weak transcription	HMEC	breast
2	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:29717600-29736400	Weak transcription	Psoas Muscle	Psoas
5	chr12:29720200-29735800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:29720200-29743600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:29722600-29736400	Weak transcription	Fetal Stomach	stomach
8	chr12:29722800-29735800	Weak transcription	Fetal Kidney	kidney
9	chr12:29725600-29735600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:29726000-29751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:29729400-29744000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:29730400-29736200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:29730600-29735600	Weak transcription	Right Ventricle	heart
14	chr12:29731000-29742600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:29731400-29735600	Weak transcription	Small Intestine	intestine
16	chr12:29731800-29769600	Weak transcription	Hela-S3	cervix
17	chr12:29732000-29737200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:29732200-29737200	Enhancers	Colon Smooth Muscle	Colon
19	chr12:29733600-29736000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr12:29733600-29737000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:29733800-29735800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:29733800-29737200	Enhancers	Adipose Nuclei	Adipose
23	chr12:29734000-29735600	Enhancers	Stomach Smooth Muscle	stomach
24	chr12:29734000-29736600	Enhancers	Brain Anterior Caudate	brain
25	chr12:29734200-29737200	Enhancers	Rectal Smooth Muscle	rectum
26	chr12:29734400-29736200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:29734600-29735800	Enhancers	Liver	Liver
28	chr12:29734600-29737000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr12:29734600-29737000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr12:29734600-29737200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:29734800-29735600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:29734800-29735800	Enhancers	NH-A	brain
33	chr12:29734800-29736000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
34	chr12:29734800-29736200	Enhancers	Brain Substantia Nigra	brain
35	chr12:29734800-29736800	Enhancers	NHLF	lung
36	chr12:29734800-29737200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:29735000-29735600	Enhancers	Osteobl	bone
38	chr12:29735000-29735800	Enhancers	NHDF-Ad	bronchial
39	chr12:29735000-29736000	Enhancers	HUVEC	blood vessel
40	chr12:29735000-29736200	Enhancers	Ovary	ovary
41	chr12:29735200-29735600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:29735200-29735600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr12:29735200-29735800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:29735200-29735800	Enhancers	Aorta	Aorta
45	chr12:29735200-29735800	Enhancers	Stomach Mucosa	stomach
46	chr12:29735200-29736000	Enhancers	Brain Hippocampus Middle	brain
47	chr12:29735200-29736000	Genic enhancers	Fetal Muscle Leg	muscle
48	chr12:29735200-29736000	Enhancers	Right Atrium	heart
49	chr12:29735200-29736000	Enhancers	HSMM	muscle
50	chr12:29735200-29736600	Enhancers	Brain Cingulate Gyrus	brain

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