Variant report

Variant	rs254227
Chromosome Location	chr5:115885574-115885575
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs153638	0.90[ASN][1000 genomes]
rs153640	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs153641	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs254076	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs254077	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs254080	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs254081	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs254206	0.82[ASN][1000 genomes]
rs254207	0.82[ASN][1000 genomes]
rs254208	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs254209	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs254210	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs254226	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs254229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs254233	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs254234	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs254227	SEMA6A	cis	cerebellum	SCAN

Chromatin state (count:52 , 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	chr5:115876400-115886200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:115878200-115893200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr5:115880000-115890400	Weak transcription	Colonic Mucosa	Colon
6	chr5:115880800-115900600	Weak transcription	Fetal Kidney	kidney
7	chr5:115881000-115886200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:115881000-115888200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:115881000-115889000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:115881600-115886200	Weak transcription	Placenta	Placenta
11	chr5:115881600-115888400	Enhancers	Fetal Intestine Large	intestine
12	chr5:115881800-115889000	Enhancers	Brain Hippocampus Middle	brain
13	chr5:115882200-115886400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:115882200-115890200	Weak transcription	Fetal Stomach	stomach
15	chr5:115882400-115886600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:115882400-115888600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:115882600-115885800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:115882600-115886200	Weak transcription	Psoas Muscle	Psoas
19	chr5:115882600-115888200	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:115882600-115890400	Weak transcription	HepG2	liver
21	chr5:115882600-115890800	Weak transcription	Aorta	Aorta
22	chr5:115882600-115895400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:115882800-115887200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:115883000-115887400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:115883800-115890400	Weak transcription	Gastric	stomach
26	chr5:115884000-115886600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr5:115884000-115886600	Weak transcription	Small Intestine	intestine
28	chr5:115884000-115889000	Weak transcription	Left Ventricle	heart
29	chr5:115884000-115890000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:115884200-115886200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:115884200-115886200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr5:115884200-115886600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:115884200-115888600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:115884200-115889000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:115884400-115889200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:115884600-115886200	Weak transcription	Brain Angular Gyrus	brain
37	chr5:115884800-115893200	Enhancers	Brain Cingulate Gyrus	brain
38	chr5:115885000-115885600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:115885000-115887200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:115885000-115888000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:115885000-115889000	Enhancers	Brain Anterior Caudate	brain
42	chr5:115885200-115886200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:115885200-115886200	Weak transcription	Brain Substantia Nigra	brain
44	chr5:115885200-115887200	Weak transcription	Fetal Intestine Small	intestine
45	chr5:115885400-115885800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr5:115885400-115885800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:115885400-115885800	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr5:115885400-115886000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr5:115885400-115886800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:115885400-115890200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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