Variant report

Variant	rs6539267
Chromosome Location	chr12:106785554-106785555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11112977	0.95[ASN][1000 genomes]
rs11112997	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579099	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581541	0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs12581936	0.95[ASN][1000 genomes]
rs12831519	0.87[ASW][hapmap]
rs17217845	0.87[ASW][hapmap];0.82[AMR][1000 genomes]
rs34762209	0.82[AMR][1000 genomes]
rs3851634	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4964175	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Tourette syndrome	22889924	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6539267	STMN1	trans	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106752400-106791600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:106753000-106788800	Weak transcription	Thymus	Thymus
3	chr12:106753000-106791600	Weak transcription	Esophagus	oesophagus
4	chr12:106753000-106793200	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:106753000-106811800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:106753000-106815400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:106755000-106789000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:106755400-106796400	Weak transcription	Spleen	Spleen
9	chr12:106764000-106821000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:106764200-106786400	Weak transcription	NHLF	lung
11	chr12:106764400-106811800	Weak transcription	HUVEC	blood vessel
12	chr12:106765000-106790600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:106767200-106808600	Weak transcription	NHDF-Ad	bronchial
14	chr12:106770800-106787400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:106772400-106789200	Weak transcription	HepG2	liver
16	chr12:106773000-106828000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:106773200-106786600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:106773200-106786600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:106773200-106786600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:106773200-106789800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:106773200-106808600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:106773800-106786600	Weak transcription	K562	blood
23	chr12:106774200-106786600	Weak transcription	NH-A	brain
24	chr12:106774400-106834000	Weak transcription	Small Intestine	intestine
25	chr12:106774600-106791600	Weak transcription	Fetal Thymus	thymus
26	chr12:106774600-106819000	Weak transcription	Right Ventricle	heart
27	chr12:106774800-106811800	Weak transcription	NHEK	skin
28	chr12:106775000-106786400	Weak transcription	GM12878-XiMat	blood
29	chr12:106775000-106786600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:106775200-106786600	Weak transcription	Fetal Intestine Large	intestine
31	chr12:106775400-106786800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:106775600-106788200	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:106776000-106786800	Weak transcription	Gastric	stomach
34	chr12:106776200-106790400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:106776400-106786600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:106776400-106788200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:106776600-106786800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:106776600-106786800	Weak transcription	Psoas Muscle	Psoas
39	chr12:106776600-106787400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:106776800-106786600	Weak transcription	Brain Germinal Matrix	brain
41	chr12:106776800-106786800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:106776800-106786800	Weak transcription	Fetal Kidney	kidney
43	chr12:106776800-106787400	Weak transcription	Colonic Mucosa	Colon
44	chr12:106776800-106788600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:106776800-106793400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:106776800-106821800	Weak transcription	Brain Angular Gyrus	brain
47	chr12:106777000-106786400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:106777000-106786600	Weak transcription	Ovary	ovary
49	chr12:106777000-106786800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:106777200-106786400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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