Variant report

Variant	rs3818380
Chromosome Location	chr13:37524255-37524256
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11147624	0.86[JPT][hapmap]
rs11147625	0.86[JPT][hapmap]
rs11147626	0.86[JPT][hapmap]
rs11147627	0.86[JPT][hapmap]
rs1127446	0.86[ASN][1000 genomes]
rs2078022	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2243710	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2323396	0.86[JPT][hapmap]
rs3852618	0.86[JPT][hapmap]
rs3852619	0.91[JPT][hapmap]
rs3864999	0.86[JPT][hapmap]
rs4054546	0.89[JPT][hapmap]
rs4943438	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4943439	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4943440	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7336575	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7989745	0.82[ASN][1000 genomes]
rs8000946	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9315455	0.88[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9469	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs9531997	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9532003	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs954370	1.00[JPT][hapmap]
rs9547708	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9547709	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9547711	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9547713	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9566172	0.99[ASN][1000 genomes]
rs9566177	0.86[JPT][hapmap]
rs9566178	0.84[JPT][hapmap]
rs9576145	0.97[ASN][1000 genomes]
rs9576146	0.93[ASN][1000 genomes]
rs9576147	0.94[ASN][1000 genomes]
rs9576149	0.92[ASN][1000 genomes]
rs9576150	0.94[ASN][1000 genomes]
rs9576151	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9576156	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs9576161	0.88[CHB][hapmap]
rs9576167	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs9576176	0.86[JPT][hapmap]
rs9576177	0.86[JPT][hapmap]
rs9576178	0.86[JPT][hapmap]
rs9576181	0.86[JPT][hapmap]
rs9603126	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv522336	chr13:37305641-37584838	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3818380	ALG5	Cis_1M	lymphoblastoid	RTeQTL
rs3818380	EXOSC8	cis	parietal	SCAN
rs3818380	FAM48A	Cis_1M	lymphoblastoid	RTeQTL
rs3818380	ALG5	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37515400-37533000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:37516800-37525200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:37517200-37538400	Weak transcription	Fetal Brain Male	brain
4	chr13:37517600-37529000	Weak transcription	Thymus	Thymus
5	chr13:37519400-37527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:37519400-37528800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr13:37519600-37525400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:37520000-37524800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:37520200-37524800	Weak transcription	Brain Angular Gyrus	brain
11	chr13:37520400-37538000	Weak transcription	Colonic Mucosa	Colon
12	chr13:37520600-37560800	Weak transcription	Small Intestine	intestine
13	chr13:37520800-37529000	Weak transcription	Gastric	stomach
14	chr13:37520800-37529400	Weak transcription	HMEC	breast
15	chr13:37520800-37538000	Weak transcription	HepG2	liver
16	chr13:37521000-37536600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr13:37521200-37538200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr13:37521400-37524600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr13:37521400-37524600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr13:37521400-37524600	Weak transcription	GM12878-XiMat	blood
21	chr13:37521400-37526800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:37521400-37527800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr13:37521400-37528600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr13:37521400-37528800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr13:37521400-37529200	Weak transcription	Fetal Kidney	kidney
26	chr13:37521400-37529400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr13:37521400-37531000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr13:37521400-37531000	Strong transcription	Liver	Liver
29	chr13:37521400-37532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:37521400-37537800	Weak transcription	NHLF	lung
31	chr13:37521400-37538000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr13:37521400-37538400	Weak transcription	Aorta	Aorta
33	chr13:37521400-37542800	Weak transcription	A549	lung
34	chr13:37521600-37525000	Weak transcription	NH-A	brain
35	chr13:37521600-37526600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr13:37521600-37527400	Strong transcription	Adipose Nuclei	Adipose
37	chr13:37521600-37527800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr13:37521600-37532600	Strong transcription	Primary T cells from cord blood	blood
39	chr13:37521600-37534800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr13:37521600-37535200	Weak transcription	NHEK	skin
41	chr13:37521600-37537800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr13:37521600-37538000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr13:37521600-37538000	Weak transcription	Brain Hippocampus Middle	brain
44	chr13:37521600-37538200	Weak transcription	HSMMtube	muscle
45	chr13:37521800-37525000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr13:37521800-37539200	Weak transcription	K562	blood
47	chr13:37522000-37531200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr13:37522000-37538000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr13:37522000-37538400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr13:37522200-37524400	Strong transcription	Muscle Satellite Cultured Cells	--

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