Variant report

Variant	rs254234
Chromosome Location	chr5:115888195-115888196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATG12-8	chr5:115887966-115890185	NONHSAT103374

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs153638	0.92[ASN][1000 genomes]
rs153640	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs153641	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs254076	0.95[ASN][1000 genomes]
rs254077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs254080	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs254081	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs254206	0.85[ASN][1000 genomes]
rs254207	0.85[ASN][1000 genomes]
rs254208	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs254209	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs254210	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs254226	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs254227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs254229	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs254233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs254234	SEMA6A	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115871000-115890400	Weak transcription	Pancreas	Pancrea
2	chr5:115873200-115889800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:115878200-115893200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr5:115880000-115890400	Weak transcription	Colonic Mucosa	Colon
5	chr5:115880800-115900600	Weak transcription	Fetal Kidney	kidney
6	chr5:115881000-115888200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:115881000-115889000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:115881600-115888400	Enhancers	Fetal Intestine Large	intestine
9	chr5:115881800-115889000	Enhancers	Brain Hippocampus Middle	brain
10	chr5:115882200-115890200	Weak transcription	Fetal Stomach	stomach
11	chr5:115882400-115888600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:115882600-115888200	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:115882600-115890400	Weak transcription	HepG2	liver
14	chr5:115882600-115890800	Weak transcription	Aorta	Aorta
15	chr5:115882600-115895400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:115883800-115890400	Weak transcription	Gastric	stomach
17	chr5:115884000-115889000	Weak transcription	Left Ventricle	heart
18	chr5:115884000-115890000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:115884200-115888600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:115884200-115889000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:115884400-115889200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:115884800-115893200	Enhancers	Brain Cingulate Gyrus	brain
23	chr5:115885000-115889000	Enhancers	Brain Anterior Caudate	brain
24	chr5:115885400-115890200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:115885400-115894000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
26	chr5:115885400-115894600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr5:115885600-115889200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:115885800-115890200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:115885800-115893600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr5:115886200-115888400	Enhancers	H9 Cell Line	embryonic stem cell
31	chr5:115886200-115888800	Enhancers	Brain Angular Gyrus	brain
32	chr5:115886200-115888800	Enhancers	Brain Substantia Nigra	brain
33	chr5:115886200-115890000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:115886400-115888400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr5:115886600-115892200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr5:115886600-115901000	Weak transcription	Placenta	Placenta
37	chr5:115886800-115888200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
38	chr5:115886800-115888400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:115887000-115888200	Weak transcription	Psoas Muscle	Psoas
40	chr5:115887000-115889000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:115887000-115889400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr5:115887000-115890400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr5:115887200-115888600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr5:115887200-115889000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:115887400-115890600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:115887400-115891000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:115887400-115895000	Weak transcription	Lung	lung
48	chr5:115887400-115897000	Weak transcription	Small Intestine	intestine
49	chr5:115887600-115889000	Weak transcription	Colon Smooth Muscle	Colon
50	chr5:115887800-115888200	Weak transcription	Fetal Intestine Small	intestine

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