Variant report

Variant	rs3733264
Chromosome Location	chr1:160516542-160516543
allele	A/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	chr1:160516238-160516774	GM12878	blood:	n/a	n/a
2	SPI1	chr1:160516244-160517234	HL-60	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: 66 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1055880	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs11265442	0.81[CEU][hapmap]
rs11265452	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs11577695	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11583402	1.00[CEU][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11585738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11590035	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12144628	0.81[CEU][hapmap]
rs12402879	0.81[CEU][hapmap]
rs12728784	0.83[CEU][hapmap]
rs1394078	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs151607	0.88[CEU][hapmap]
rs1572382	0.81[CEU][hapmap]
rs16832283	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs17381453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385337	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs17385407	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs17385878	0.81[EUR][1000 genomes]
rs1809963	0.96[CEU][hapmap]
rs1998651	0.81[CEU][hapmap]
rs2025517	0.80[CEU][hapmap]
rs2083128	0.87[CEU][hapmap]
rs2099604	0.86[CEU][hapmap]
rs2753260	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs3733265	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];1.00[ASN][1000 genomes]
rs3733266	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs3753381	0.86[MEX][hapmap]
rs3755898	0.84[EUR][1000 genomes]
rs3766384	0.84[EUR][1000 genomes]
rs3766385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766387	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs3766388	0.96[CEU][hapmap]
rs3766389	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs3816146	0.84[CEU][hapmap]
rs4145897	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5002947	0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap]
rs56040770	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61801562	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61801564	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61801565	0.89[EUR][1000 genomes]
rs61801567	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61802603	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802604	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61802605	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61802606	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61802608	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61802610	0.86[ASN][1000 genomes]
rs6662093	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6668760	0.81[CEU][hapmap]
rs6670721	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6687641	0.88[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs6692382	0.81[CEU][hapmap]
rs6697596	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6699346	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67197441	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72708818	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72708832	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7418241	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7539982	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7547054	0.88[CEU][hapmap]
rs7550771	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs3733264	CSNK1D	trans	multi-tissue	Pritchard
rs3733264	SLAMF6	cis	lymphoblastoid	seeQTL
rs3733264	LAMB2	trans	brain	seeQTL
rs3733264	KCNN3	cis	cerebellum	SCAN
rs3733264	CD84	cis	multi-tissue	Pritchard
rs3733264	VANGL2	cis	cerebellum	SCAN
rs3733264	RAB2L	trans	multi-tissue	Pritchard
rs3733264	CBS	trans	brain	seeQTL
rs3733264	ATF6	cis	parietal	SCAN
rs3733264	OLFML2B	cis	parietal	SCAN
rs3733264	LRP1B	trans	parietal	SCAN
rs3733264	SDHC	cis	brain	seeQTL
rs3733264	ADAMTS4	cis	cerebellum	SCAN
rs3733264	NRM	trans	brain	seeQTL
rs3733264	ADAMTS4	cis	parietal	SCAN
rs3733264	CD84	cis	lymphoblastoid	seeQTL

Chromatin state (count:42 , 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	chr1:160513200-160516800	Weak transcription	Fetal Lung	lung
7	chr1:160513800-160516800	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:160514400-160519800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:160515000-160518800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:160515200-160516600	Weak transcription	Primary T cells from cord blood	blood
11	chr1:160515200-160516600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:160515200-160516600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:160515200-160517400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:160515200-160520600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:160515200-160521800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:160515400-160516600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:160516000-160516600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:160516000-160517400	Enhancers	Primary B cells from cord blood	blood
19	chr1:160516000-160517400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:160516000-160517400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:160516000-160517400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:160516000-160518600	Enhancers	K562	blood
23	chr1:160516000-160520600	Genic enhancers	Fetal Thymus	thymus
24	chr1:160516000-160526200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:160516200-160516600	Strong transcription	Thymus	Thymus
26	chr1:160516200-160516800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:160516200-160516800	Enhancers	Placenta	Placenta
28	chr1:160516200-160517200	Enhancers	Stomach Mucosa	stomach
29	chr1:160516200-160517400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:160516200-160517600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr1:160516200-160517600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:160516200-160517600	Genic enhancers	GM12878-XiMat	blood
33	chr1:160516200-160518400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:160516200-160519200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:160516200-160523800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:160516400-160516600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:160516400-160516800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr1:160516400-160516800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr1:160516400-160517000	Enhancers	Brain Hippocampus Middle	brain
40	chr1:160516400-160517800	Enhancers	Adipose Nuclei	Adipose
41	chr1:160516400-160517800	Strong transcription	Dnd41	blood
42	chr1:160516400-160520000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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