Variant report

Variant	rs9566172
Chromosome Location	chr13:37523200-37523201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

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	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2078022	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243710	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2323396	0.86[JPT][hapmap]
rs3818380	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3852618	0.86[JPT][hapmap]
rs3852619	0.91[JPT][hapmap]
rs3864999	0.86[JPT][hapmap]
rs4054546	0.89[JPT][hapmap]
rs4943438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4943439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4943440	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];0.96[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336575	0.94[ASN][1000 genomes]
rs7989745	0.81[ASN][1000 genomes]
rs8000946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9315455	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs9469	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9532003	0.92[ASN][1000 genomes]
rs954370	1.00[JPT][hapmap]
rs9547708	0.94[ASN][1000 genomes]
rs9547709	0.92[ASN][1000 genomes]
rs9547711	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9547713	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9566177	0.86[JPT][hapmap]
rs9566178	0.84[JPT][hapmap]
rs9576144	0.96[CEU][hapmap];0.80[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9576145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576146	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576147	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576149	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576150	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576151	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576156	1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap]
rs9576161	0.94[CHB][hapmap]
rs9576167	1.00[CHB][hapmap];0.87[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	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9566172	ALG5	cis	parietal	SCAN
rs9566172	MIR365-1	trans	lymphoblastoid	seeQTL
rs9566172	EXOSC8	cis	parietal	SCAN

Chromatin state (count:108 , 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	chr13:37519000-37524000	Weak transcription	Primary B cells from cord blood	blood
6	chr13:37519200-37523200	Weak transcription	NHDF-Ad	bronchial
7	chr13:37519400-37527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:37519400-37528800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr13:37519600-37525400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:37520000-37523800	Weak transcription	Placenta	Placenta
12	chr13:37520000-37524800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:37520200-37524200	Weak transcription	Fetal Thymus	thymus
14	chr13:37520200-37524800	Weak transcription	Brain Angular Gyrus	brain
15	chr13:37520400-37538000	Weak transcription	Colonic Mucosa	Colon
16	chr13:37520600-37560800	Weak transcription	Small Intestine	intestine
17	chr13:37520800-37523200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:37520800-37529000	Weak transcription	Gastric	stomach
19	chr13:37520800-37529400	Weak transcription	HMEC	breast
20	chr13:37520800-37538000	Weak transcription	HepG2	liver
21	chr13:37521000-37536600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr13:37521200-37524200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:37521200-37538200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:37521400-37523200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr13:37521400-37524600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr13:37521400-37524600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr13:37521400-37524600	Weak transcription	GM12878-XiMat	blood
28	chr13:37521400-37526800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:37521400-37527800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:37521400-37528600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr13:37521400-37528800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr13:37521400-37529200	Weak transcription	Fetal Kidney	kidney
33	chr13:37521400-37529400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr13:37521400-37531000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:37521400-37531000	Strong transcription	Liver	Liver
36	chr13:37521400-37532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:37521400-37537800	Weak transcription	NHLF	lung
38	chr13:37521400-37538000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr13:37521400-37538400	Weak transcription	Aorta	Aorta
40	chr13:37521400-37542800	Weak transcription	A549	lung
41	chr13:37521600-37523400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr13:37521600-37523600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr13:37521600-37523600	Strong transcription	Fetal Stomach	stomach
44	chr13:37521600-37525000	Weak transcription	NH-A	brain
45	chr13:37521600-37526600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr13:37521600-37527400	Strong transcription	Adipose Nuclei	Adipose
47	chr13:37521600-37527800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr13:37521600-37532600	Strong transcription	Primary T cells from cord blood	blood
49	chr13:37521600-37534800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr13:37521600-37535200	Weak transcription	NHEK	skin

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