Variant report

Variant	rs417406
Chromosome Location	chr11:16873799-16873800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:16868421..16871195-chr11:16872286..16874051,3	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10741713	0.82[JPT][hapmap]
rs10766360	0.82[JPT][hapmap]
rs12418111	0.82[JPT][hapmap]
rs1638456	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1638457	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16933675	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs16933680	0.82[JPT][hapmap]
rs16933682	0.82[JPT][hapmap]
rs16933683	0.82[JPT][hapmap]
rs16933684	0.82[JPT][hapmap]
rs177561	0.82[JPT][hapmap]
rs177562	0.82[JPT][hapmap]
rs177563	0.82[JPT][hapmap]
rs2057788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2190752	0.81[JPT][hapmap]
rs2883150	0.82[JPT][hapmap]
rs369457	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]
rs370053	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs370671	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs371905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs373266	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs376641	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs378863	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs379051	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs380655	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs381815	0.88[JPT][hapmap]
rs382280	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs385627	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs385943	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs387849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs389967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs390974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs391332	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs392706	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs393633	0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs397343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs397373	0.91[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs398216	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs400085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs400349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs400458	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs401820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs402982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404492	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs406109	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs406890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs406937	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs407354	0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs407932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs409354	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs414219	0.88[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs414992	0.88[JPT][hapmap]
rs415265	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs417349	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs418034	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs420975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs425325	0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs425745	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs426085	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs427429	0.82[AMR][1000 genomes]
rs428840	0.87[JPT][hapmap]
rs428933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs429368	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs430211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs431208	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs432046	0.91[CEU][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs432656	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs433212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs433225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs434761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs434899	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs435206	0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs439224	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs440212	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs443327	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs445146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs445205	0.91[CEU][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs445431	0.81[AMR][1000 genomes]
rs446518	0.90[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs446612	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs448671	0.88[JPT][hapmap]
rs450828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs452414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs452745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs453015	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs454538	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs454869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756875	0.81[JPT][hapmap]
rs4756876	0.82[JPT][hapmap]
rs4757449	0.82[JPT][hapmap]
rs4757451	0.82[JPT][hapmap]
rs4757454	0.82[JPT][hapmap]
rs4757456	0.82[JPT][hapmap]
rs4757457	0.82[JPT][hapmap]
rs58555284	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6486326	0.82[JPT][hapmap]
rs7111470	0.82[JPT][hapmap]
rs7924696	0.82[JPT][hapmap]
rs7926335	0.82[JPT][hapmap]
rs7939987	0.82[JPT][hapmap]
rs7951328	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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
rs417406	PTPN5	cis	cerebellum	SCAN
rs417406	SAA1	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16839200-16878800	Weak transcription	Thymus	Thymus
2	chr11:16843000-16874600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:16846600-16874000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:16848200-16875200	Weak transcription	Right Ventricle	heart
5	chr11:16848400-16878600	Weak transcription	Small Intestine	intestine
6	chr11:16853400-16883800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:16855200-16877600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:16855200-16878800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:16858000-16876800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:16858200-16878800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:16858400-16876400	Weak transcription	Brain Germinal Matrix	brain
12	chr11:16861200-16879800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr11:16861800-16877000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr11:16861800-16880600	Weak transcription	HMEC	breast
15	chr11:16862200-16875200	Genic enhancers	Fetal Heart	heart
16	chr11:16862200-16876800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:16863400-16875600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:16863400-16875600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:16863400-16882000	Weak transcription	Stomach Mucosa	stomach
20	chr11:16863800-16875800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:16863800-16884800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:16863800-16892600	Weak transcription	Fetal Kidney	kidney
23	chr11:16864000-16878800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:16864200-16882000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:16866800-16879000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:16867600-16879200	Strong transcription	Liver	Liver
27	chr11:16867800-16885000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr11:16869200-16876200	Weak transcription	HSMMtube	muscle
29	chr11:16869600-16876200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:16869800-16875600	Weak transcription	Spleen	Spleen
31	chr11:16870000-16874000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:16870400-16878000	Strong transcription	Fetal Intestine Large	intestine
33	chr11:16870800-16879000	Strong transcription	HepG2	liver
34	chr11:16871000-16874000	Strong transcription	Ovary	ovary
35	chr11:16871200-16874000	Strong transcription	Esophagus	oesophagus
36	chr11:16871200-16878000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr11:16871400-16873800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:16871400-16874000	Strong transcription	Gastric	stomach
39	chr11:16871400-16878800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr11:16871400-16879000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:16871400-16879000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr11:16871600-16875000	Weak transcription	Left Ventricle	heart
43	chr11:16871600-16875000	Weak transcription	Right Atrium	heart
44	chr11:16871600-16875600	Weak transcription	Fetal Muscle Leg	muscle
45	chr11:16871600-16876800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:16871600-16877000	Strong transcription	A549	lung
47	chr11:16871800-16874800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:16871800-16875200	Weak transcription	Fetal Brain Female	brain
49	chr11:16872000-16875000	Weak transcription	Brain Anterior Caudate	brain
50	chr11:16872000-16875000	Weak transcription	Stomach Smooth Muscle	stomach

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