Variant report

Variant	rs369457
Chromosome Location	chr11:16863049-16863050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10741713	0.88[JPT][hapmap]
rs10766360	0.88[JPT][hapmap]
rs11024087	0.87[JPT][hapmap]
rs12418111	0.88[JPT][hapmap]
rs1638457	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16933675	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs16933680	0.88[JPT][hapmap]
rs16933682	0.88[JPT][hapmap]
rs16933683	0.88[JPT][hapmap]
rs16933684	0.88[JPT][hapmap]
rs177561	0.88[JPT][hapmap]
rs177562	0.88[JPT][hapmap]
rs177563	0.88[JPT][hapmap]
rs2057788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2190752	0.88[JPT][hapmap]
rs2883150	0.88[JPT][hapmap]
rs370053	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs370671	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs371905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373266	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378863	0.82[AMR][1000 genomes]
rs379051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs380655	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs381815	0.94[JPT][hapmap]
rs382280	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs385627	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs385943	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs387849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs388968	0.86[JPT][hapmap]
rs389967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs390974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs392706	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393633	0.91[CEU][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs397343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs397373	0.91[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs398216	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs400085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs400349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs400458	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs401820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs402982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs404492	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs406109	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs406890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs406937	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs407354	0.91[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs407932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs409354	1.00[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs414219	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs414992	0.94[JPT][hapmap]
rs415265	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs417406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs418034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs420975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs425325	0.91[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs425745	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426085	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs428840	0.94[JPT][hapmap]
rs428933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429368	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431208	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs432046	0.91[CEU][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap]
rs432656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs433212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs433225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434899	0.87[JPT][hapmap]
rs435206	0.93[JPT][hapmap]
rs439224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs440212	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs443327	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445205	0.91[CEU][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs446518	0.90[CEU][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs446612	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448671	0.94[JPT][hapmap]
rs450828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs452414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs453015	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs454538	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs454869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4756875	0.88[JPT][hapmap]
rs4756876	0.88[JPT][hapmap]
rs4757449	0.88[JPT][hapmap]
rs4757451	0.88[JPT][hapmap]
rs4757452	0.87[JPT][hapmap]
rs4757454	0.88[JPT][hapmap]
rs4757456	0.88[JPT][hapmap]
rs4757457	0.88[JPT][hapmap]
rs58555284	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486314	0.83[YRI][hapmap]
rs6486326	0.88[JPT][hapmap]
rs7111470	0.88[JPT][hapmap]
rs7396552	0.83[JPT][hapmap]
rs7481080	0.83[JPT][hapmap]
rs7924696	0.88[JPT][hapmap]
rs7926335	0.88[JPT][hapmap]
rs7939987	0.88[JPT][hapmap]
rs7951328	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs369457	SAA1	cis	parietal	SCAN
rs369457	PTPN5	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16813200-16871400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:16823000-16871400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:16839200-16878800	Weak transcription	Thymus	Thymus
4	chr11:16842600-16873400	Weak transcription	Hela-S3	cervix
5	chr11:16843000-16874600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:16846600-16874000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:16847000-16864000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:16847000-16871200	Weak transcription	Brain Substantia Nigra	brain
9	chr11:16847200-16871400	Weak transcription	Brain Hippocampus Middle	brain
10	chr11:16847800-16865000	Weak transcription	Fetal Muscle Leg	muscle
11	chr11:16847800-16871600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:16848200-16871400	Weak transcription	Aorta	Aorta
13	chr11:16848200-16875200	Weak transcription	Right Ventricle	heart
14	chr11:16848400-16866600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:16848400-16878600	Weak transcription	Small Intestine	intestine
16	chr11:16848600-16868400	Weak transcription	HSMMtube	muscle
17	chr11:16849800-16865400	Strong transcription	Fetal Intestine Small	intestine
18	chr11:16849800-16871400	Weak transcription	Pancreas	Pancrea
19	chr11:16850400-16871200	Weak transcription	Fetal Brain Female	brain
20	chr11:16850600-16865600	Weak transcription	Psoas Muscle	Psoas
21	chr11:16850600-16871800	Weak transcription	Colonic Mucosa	Colon
22	chr11:16850800-16870600	Weak transcription	Fetal Brain Male	brain
23	chr11:16853400-16883800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:16854000-16868000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:16855000-16863400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:16855200-16863600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:16855200-16873000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:16855200-16877600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:16855200-16878800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:16856200-16863200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:16858000-16876800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:16858200-16871600	Weak transcription	A549	lung
33	chr11:16858200-16878800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr11:16858400-16876400	Weak transcription	Brain Germinal Matrix	brain
35	chr11:16858800-16863400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:16859200-16868800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:16860000-16870000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:16861000-16864000	Strong transcription	Fetal Intestine Large	intestine
39	chr11:16861200-16863200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:16861200-16863400	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr11:16861200-16864000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr11:16861200-16864000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr11:16861200-16864200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr11:16861200-16879800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr11:16861400-16863600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:16861400-16863800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr11:16861400-16863800	Strong transcription	Placenta	Placenta
48	chr11:16861400-16864000	Strong transcription	Fetal Stomach	stomach
49	chr11:16861400-16864000	Strong transcription	Ovary	ovary
50	chr11:16861400-16864400	Strong transcription	Liver	Liver

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