Variant report

Variant	rs28393472
Chromosome Location	chr15:41684425-41684426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10152497	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10153010	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10467974	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10518718	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11549913	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11630191	0.89[ASN][1000 genomes]
rs11631770	0.88[ASN][1000 genomes]
rs11633799	0.84[ASN][1000 genomes]
rs12324291	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16971767	0.89[ASN][1000 genomes]
rs16971798	0.93[ASN][1000 genomes]
rs16971806	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16971832	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16971834	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757455	0.81[ASN][1000 genomes]
rs2015781	0.91[ASN][1000 genomes]
rs2777491	0.88[ASN][1000 genomes]
rs28526381	0.89[ASN][1000 genomes]
rs28578057	0.89[ASN][1000 genomes]
rs28583065	0.89[ASN][1000 genomes]
rs28600680	0.96[ASN][1000 genomes]
rs28643296	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28655070	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28716108	0.92[ASN][1000 genomes]
rs28792672	0.93[ASN][1000 genomes]
rs28847691	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316605	0.81[ASN][1000 genomes]
rs316609	0.88[ASN][1000 genomes]
rs316610	0.82[ASN][1000 genomes]
rs316613	0.86[ASN][1000 genomes]
rs316614	0.86[ASN][1000 genomes]
rs316615	0.83[ASN][1000 genomes]
rs35826725	0.93[ASN][1000 genomes]
rs3743038	0.96[ASN][1000 genomes]
rs55782852	0.89[ASN][1000 genomes]
rs58335029	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58910172	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59590312	0.93[ASN][1000 genomes]
rs61037359	0.88[ASN][1000 genomes]
rs61127691	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6650519	0.87[ASN][1000 genomes]
rs66538814	0.96[ASN][1000 genomes]
rs7161772	0.89[ASN][1000 genomes]
rs7163649	0.88[ASN][1000 genomes]
rs7163788	0.91[ASN][1000 genomes]
rs7165675	0.89[ASN][1000 genomes]
rs7167498	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7167729	0.91[ASN][1000 genomes]
rs7168177	0.89[ASN][1000 genomes]
rs7172148	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175690	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175800	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176314	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176505	0.82[ASN][1000 genomes]
rs7176588	0.88[ASN][1000 genomes]
rs7177641	0.88[ASN][1000 genomes]
rs7180492	0.84[ASN][1000 genomes]
rs7181560	0.84[ASN][1000 genomes]
rs7181911	0.96[ASN][1000 genomes]
rs7182667	0.95[ASN][1000 genomes]
rs7182700	0.85[ASN][1000 genomes]
rs7183337	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73404980	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73404987	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73404994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404995	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404996	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405000	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73405001	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73407109	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023619	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8026197	0.91[ASN][1000 genomes]
rs8027626	0.91[ASN][1000 genomes]
rs8032838	0.89[ASN][1000 genomes]
rs8034626	0.87[ASN][1000 genomes]
rs8034819	0.93[ASN][1000 genomes]
rs8036498	0.89[ASN][1000 genomes]
rs8036527	0.81[ASN][1000 genomes]
rs8037824	0.89[ASN][1000 genomes]
rs823716	0.83[ASN][1000 genomes]
rs919961	0.93[ASN][1000 genomes]
rs9302109	0.89[ASN][1000 genomes]
rs9672866	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9972288	0.93[ASN][1000 genomes]
rs9972547	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
5	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41625800-41694200	Weak transcription	Small Intestine	intestine
2	chr15:41626800-41686400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:41660200-41688400	Weak transcription	Esophagus	oesophagus
4	chr15:41660200-41693800	Weak transcription	Right Ventricle	heart
5	chr15:41661800-41693200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:41665200-41688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:41666400-41686400	Weak transcription	Brain Anterior Caudate	brain
8	chr15:41669000-41687000	Weak transcription	Aorta	Aorta
9	chr15:41670600-41686400	Weak transcription	NH-A	brain
10	chr15:41670800-41686400	Weak transcription	Gastric	stomach
11	chr15:41672000-41693600	Weak transcription	Colonic Mucosa	Colon
12	chr15:41673200-41688400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:41673400-41687000	Weak transcription	K562	blood
14	chr15:41673400-41687200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:41673400-41693800	Weak transcription	HMEC	breast
16	chr15:41673600-41686600	Weak transcription	GM12878-XiMat	blood
17	chr15:41673600-41687000	Weak transcription	HUVEC	blood vessel
18	chr15:41673600-41687200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:41673600-41693800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr15:41673600-41693800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:41673800-41685000	Weak transcription	HSMM	muscle
22	chr15:41673800-41686200	Weak transcription	Fetal Lung	lung
23	chr15:41673800-41686400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:41673800-41686400	Weak transcription	NHEK	skin
25	chr15:41673800-41686600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:41673800-41686600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:41673800-41687000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:41673800-41687000	Weak transcription	A549	lung
29	chr15:41673800-41687000	Weak transcription	Dnd41	blood
30	chr15:41673800-41688400	Weak transcription	Hela-S3	cervix
31	chr15:41673800-41693600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:41674000-41685000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:41674000-41686400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:41674000-41693800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:41674000-41693800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:41674200-41686400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:41675400-41686400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:41676400-41689400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:41676400-41689400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr15:41676400-41689400	Strong transcription	Fetal Thymus	thymus
41	chr15:41676400-41692200	Strong transcription	Fetal Stomach	stomach
42	chr15:41676600-41686800	Weak transcription	Colon Smooth Muscle	Colon
43	chr15:41676800-41686600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:41677000-41686400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:41677000-41693400	Weak transcription	HepG2	liver
46	chr15:41677200-41693400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:41678200-41689200	Strong transcription	Liver	Liver
48	chr15:41678400-41687000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr15:41678400-41693800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:41678800-41686400	Weak transcription	HSMMtube	muscle

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