Variant report

Variant	rs254080
Chromosome Location	chr5:115889776-115889777
allele	A/G
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: 0)

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

rs_ID	r²[population]
rs153638	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs153640	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs153641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs254076	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254077	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254081	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs254206	0.89[ASN][1000 genomes]
rs254207	0.89[ASN][1000 genomes]
rs254208	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs254209	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs254210	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs254226	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs254227	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]
rs254229	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs254233	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs254234	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]

No data

Chromatin state (count:60 , 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	chr5:115882200-115890200	Weak transcription	Fetal Stomach	stomach
7	chr5:115882600-115890400	Weak transcription	HepG2	liver
8	chr5:115882600-115890800	Weak transcription	Aorta	Aorta
9	chr5:115882600-115895400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:115883800-115890400	Weak transcription	Gastric	stomach
11	chr5:115884000-115890000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:115884800-115893200	Enhancers	Brain Cingulate Gyrus	brain
13	chr5:115885400-115890200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:115885400-115894000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
15	chr5:115885400-115894600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:115885800-115890200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:115885800-115893600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr5:115886200-115890000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:115886600-115892200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr5:115886600-115901000	Weak transcription	Placenta	Placenta
21	chr5:115887000-115890400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:115887400-115890600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:115887400-115891000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:115887400-115895000	Weak transcription	Lung	lung
25	chr5:115887400-115897000	Weak transcription	Small Intestine	intestine
26	chr5:115888400-115890400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:115888400-115893800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:115888600-115891000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:115888800-115890000	Weak transcription	Brain Angular Gyrus	brain
30	chr5:115888800-115891200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr5:115889000-115890000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:115889000-115890800	Enhancers	Colon Smooth Muscle	Colon
33	chr5:115889000-115895200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr5:115889200-115889800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:115889200-115890400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:115889200-115890400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
37	chr5:115889200-115891400	Enhancers	Fetal Intestine Large	intestine
38	chr5:115889200-115891800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr5:115889200-115892600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr5:115889200-115893600	Enhancers	Brain Substantia Nigra	brain
41	chr5:115889400-115889800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:115889400-115890400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:115889400-115890400	Weak transcription	Brain Germinal Matrix	brain
44	chr5:115889400-115890400	Weak transcription	Fetal Lung	lung
45	chr5:115889400-115890400	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:115889400-115890400	Weak transcription	Left Ventricle	heart
47	chr5:115889400-115890400	Weak transcription	Ovary	ovary
48	chr5:115889400-115890600	Weak transcription	Psoas Muscle	Psoas
49	chr5:115889400-115891000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr5:115889400-115891600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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