Variant report

Variant	rs420975
Chromosome Location	chr11:16848522-16848523
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	chr11:16847181..16850081-chr11:17095305..17097165,2	K562	blood:

Variant related genes	Relation type
ENSG00000110700	Chromatin interaction
ENSG00000221322	Chromatin interaction
ENSG00000272034	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10741713	0.88[JPT][hapmap]
rs10766360	0.88[JPT][hapmap]
rs11024087	0.87[JPT][hapmap]
rs12418111	0.88[JPT][hapmap]
rs1638456	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1638457	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16933675	0.88[CHB][hapmap];0.88[JPT][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];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2190752	0.88[JPT][hapmap]
rs2883150	0.88[JPT][hapmap]
rs366590	0.86[LWK][hapmap]
rs369457	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]
rs370053	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370671	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs371905	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];1.00[ASN][1000 genomes]
rs373266	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs376641	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs378863	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs379051	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380655	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs381815	0.94[JPT][hapmap]
rs382280	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385627	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs385943	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs387849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388968	0.86[JPT][hapmap]
rs389967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs390974	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];1.00[ASN][1000 genomes]
rs391332	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs392706	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs393633	0.91[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs397343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs397373	0.91[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs398216	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs400085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400458	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs401820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404492	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406109	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406937	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs407354	0.91[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs407932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409354	1.00[CEU][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes]
rs414219	0.94[JPT][hapmap];0.81[TSI][hapmap]
rs414992	0.94[JPT][hapmap]
rs415265	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs417349	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417406	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]
rs418034	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425325	0.91[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs425745	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs426085	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs428840	0.94[JPT][hapmap]
rs428933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429368	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs430211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs431208	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs432046	0.91[CEU][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs432656	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433225	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];1.00[ASN][1000 genomes]
rs434761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434899	0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs435206	0.93[JPT][hapmap]
rs439224	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440212	1.00[CEU][hapmap];0.90[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];0.96[ASN][1000 genomes]
rs443327	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445205	0.91[CEU][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs446518	0.90[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs446612	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs448671	0.94[JPT][hapmap]
rs450828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs452414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs452745	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];0.95[ASN][1000 genomes]
rs453015	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs454538	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs454869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[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	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
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	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[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
rs420975	PTPN5	cis	cerebellum	SCAN
rs420975	SAA1	cis	parietal	SCAN

Chromatin state (count:66 , 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	chr11:16836000-16861600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr11:16837200-16848600	Weak transcription	Brain Germinal Matrix	brain
5	chr11:16839200-16878800	Weak transcription	Thymus	Thymus
6	chr11:16842400-16862200	Weak transcription	Fetal Kidney	kidney
7	chr11:16842600-16852600	Weak transcription	Placenta	Placenta
8	chr11:16842600-16853600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:16842600-16854200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:16842600-16855000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:16842600-16873400	Weak transcription	Hela-S3	cervix
12	chr11:16842800-16862200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:16843000-16874600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:16844000-16862000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:16844400-16861200	Weak transcription	HMEC	breast
16	chr11:16845000-16850600	Genic enhancers	Fetal Heart	heart
17	chr11:16845800-16855200	Strong transcription	HepG2	liver
18	chr11:16846000-16850600	Strong transcription	Liver	Liver
19	chr11:16846200-16849000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr11:16846200-16849200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr11:16846200-16857800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:16846400-16852800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:16846600-16874000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr11:16846800-16849200	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:16846800-16850800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:16847000-16864000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:16847000-16871200	Weak transcription	Brain Substantia Nigra	brain
28	chr11:16847200-16871400	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:16847400-16848600	Strong transcription	Pancreas	Pancrea
30	chr11:16847400-16849600	Enhancers	Stomach Mucosa	stomach
31	chr11:16847600-16850600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:16847600-16852800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:16847600-16857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:16847800-16853000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:16847800-16865000	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:16847800-16871600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr11:16848000-16848600	Strong transcription	HSMMtube	muscle
38	chr11:16848000-16849800	Genic enhancers	Gastric	stomach
39	chr11:16848000-16850600	Strong transcription	Colonic Mucosa	Colon
40	chr11:16848000-16853000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:16848000-16853800	Weak transcription	Right Atrium	heart
42	chr11:16848000-16854200	Weak transcription	Brain Anterior Caudate	brain
43	chr11:16848000-16862400	Weak transcription	Adipose Nuclei	Adipose
44	chr11:16848000-16863000	Weak transcription	Lung	lung
45	chr11:16848200-16849800	Enhancers	Duodenum Mucosa	Duodenum
46	chr11:16848200-16853000	Weak transcription	A549	lung
47	chr11:16848200-16853400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr11:16848200-16853800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:16848200-16854200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:16848200-16854200	Weak transcription	Left Ventricle	heart

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