Variant report

Variant	rs3766389
Chromosome Location	chr1:160517214-160517215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:160517165-160520133	GM12878	blood:	n/a	n/a
2	SPI1	chr1:160516244-160517234	HL-60	blood:	n/a	n/a
3	MTA3	chr1:160517014-160521352	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:160517210-160520130	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:160517214-160518546	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:160517170-160518592	GM12892	blood:	n/a	n/a
7	MTA3	chr1:160517152-160518695	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:160517136-160518635	GM12878	blood:	n/a	n/a
9	STAT5A	chr1:160517207-160518707	GM12878	blood:	n/a	n/a
10	NFATC1	chr1:160517196-160518466	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160515112..160518077-chr1:160519420..160523438,5	K562	blood:

Variant related genes	Relation type
ENSG00000264286	TF binding region
ENSG00000066294	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1055880	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265424	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11265442	0.81[CEU][hapmap]
rs11265452	0.96[CEU][hapmap]
rs11583402	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11585738	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs11590035	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs12144628	0.81[CEU][hapmap]
rs12402879	0.81[CEU][hapmap]
rs12728784	0.83[CEU][hapmap]
rs1394078	1.00[CEU][hapmap]
rs151607	0.88[CEU][hapmap]
rs1572382	0.81[CEU][hapmap]
rs16832283	0.96[CEU][hapmap]
rs1726	0.82[EUR][1000 genomes]
rs17381453	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs17385337	0.92[CEU][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes]
rs17385407	1.00[CEU][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs1809963	0.96[CEU][hapmap]
rs1998651	0.81[CEU][hapmap]
rs2025517	0.80[CEU][hapmap]
rs2083128	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2099604	0.86[CEU][hapmap]
rs2753260	0.88[CEU][hapmap]
rs3733264	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs3733265	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs3733266	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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755898	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766384	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766385	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3766387	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766388	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs3816146	0.84[CEU][hapmap]
rs4145897	0.86[EUR][1000 genomes]
rs5002947	0.96[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs55917218	0.80[AMR][1000 genomes]
rs56040770	0.82[EUR][1000 genomes]
rs61801565	0.81[EUR][1000 genomes]
rs61801567	0.81[EUR][1000 genomes]
rs61802604	0.82[EUR][1000 genomes]
rs61802605	0.86[EUR][1000 genomes]
rs61802606	0.89[EUR][1000 genomes]
rs61802608	0.88[EUR][1000 genomes]
rs6668760	0.81[CEU][hapmap]
rs6670721	0.96[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6687641	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6692382	0.81[CEU][hapmap]
rs6697596	0.81[EUR][1000 genomes]
rs67197441	0.88[EUR][1000 genomes]
rs72708832	0.88[EUR][1000 genomes]
rs7418241	0.86[EUR][1000 genomes]
rs7539982	0.82[EUR][1000 genomes]
rs7547054	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7550771	0.88[CEU][hapmap];0.83[GIH][hapmap]
rs912582	1.00[CEU][hapmap]
rs977019	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs3766389	PLAU	trans	brain	seeQTL
rs3766389	SDHC	cis	brain	seeQTL
rs3766389	SLAMF6	cis	lymphoblastoid	seeQTL
rs3766389	PEX19	cis	brain	seeQTL
rs3766389	VANGL2	cis	cerebellum	SCAN
rs3766389	ADAMTS4	cis	parietal	SCAN
rs3766389	LAMB2	trans	brain	seeQTL
rs3766389	CBS	trans	brain	seeQTL
rs3766389	PAK4	trans	brain	seeQTL
rs3766389	RAB2L	trans	multi-tissue	Pritchard
rs3766389	ADAMTS4	cis	cerebellum	SCAN
rs3766389	CD84	cis	lymphoblastoid	seeQTL
rs3766389	RAVER1	trans	brain	seeQTL
rs3766389	LRP1B	trans	parietal	SCAN
rs3766389	ATF6	cis	parietal	SCAN
rs3766389	KCNN3	cis	cerebellum	SCAN
rs3766389	CSNK1D	trans	multi-tissue	Pritchard
rs3766389	OLFML2B	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160510200-160520400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:160511800-160517800	Weak transcription	Pancreas	Pancrea
3	chr1:160511800-160522400	Weak transcription	Gastric	stomach
4	chr1:160511800-160527800	Weak transcription	Colonic Mucosa	Colon
5	chr1:160512200-160524600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:160514400-160519800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:160515000-160518800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:160515200-160517400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:160515200-160520600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:160515200-160521800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:160516000-160517400	Enhancers	Primary B cells from cord blood	blood
12	chr1:160516000-160517400	Strong transcription	Primary hematopoietic stem cells	blood
13	chr1:160516000-160517400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:160516000-160517400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:160516000-160518600	Enhancers	K562	blood
16	chr1:160516000-160520600	Genic enhancers	Fetal Thymus	thymus
17	chr1:160516000-160526200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:160516200-160517400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:160516200-160517600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:160516200-160517600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:160516200-160517600	Genic enhancers	GM12878-XiMat	blood
22	chr1:160516200-160518400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:160516200-160519200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:160516200-160523800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:160516400-160517800	Enhancers	Adipose Nuclei	Adipose
26	chr1:160516400-160517800	Strong transcription	Dnd41	blood
27	chr1:160516400-160520000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:160516600-160517400	Weak transcription	Thymus	Thymus
29	chr1:160516600-160517600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:160516600-160518000	Strong transcription	Primary T cells from cord blood	blood
31	chr1:160516600-160518000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:160516600-160518000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:160516600-160518000	Enhancers	Fetal Brain Female	brain
34	chr1:160516600-160520400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:160516600-160523800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:160516800-160517800	Enhancers	Fetal Lung	lung
37	chr1:160516800-160518000	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr1:160516800-160518000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:160516800-160520600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:160517000-160517400	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:160517000-160517400	Enhancers	Placenta	Placenta
42	chr1:160517000-160520600	Enhancers	Spleen	Spleen
43	chr1:160517200-160517600	Genic enhancers	Rectal Mucosa Donor 29	rectum
44	chr1:160517200-160518600	Weak transcription	Stomach Mucosa	stomach

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