Variant report

Variant	rs3766385
Chromosome Location	chr1:160519413-160519414
allele	A/G
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	STAT5A	chr1:160518818-160519533	GM12878	blood:	n/a	n/a
2	BCL3	chr1:160518995-160519780	GM12878	blood:	n/a	n/a
3	TBL1XR1	chr1:160519089-160519540	GM12878	blood:	n/a	n/a
4	RELA	chr1:160518975-160519615	GM10847	blood:	n/a	n/a
5	EBF1	chr1:160518939-160519875	GM12878	blood:	n/a	chr1:160519608-160519618 chr1:160519608-160519617 chr1:160519606-160519619
6	NFIC	chr1:160518889-160519726	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:160518974-160519563	GM12891	blood:	n/a	n/a
8	POLR2A	chr1:160518811-160519590	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:160518774-160519585	GM12891	blood:	n/a	n/a
10	STAT5A	chr1:160518809-160519741	GM12878	blood:	n/a	n/a
11	NFIC	chr1:160517165-160520133	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:160517886-160519626	GM12891	blood:	n/a	n/a
13	RELA	chr1:160518997-160519737	GM12891	blood:	n/a	n/a
14	YY1	chr1:160519052-160519501	GM12878	blood:	n/a	n/a
15	NFATC1	chr1:160518496-160519709	GM12878	blood:	n/a	n/a
16	EBF1	chr1:160519107-160520026	GM12878	blood:	n/a	chr1:160519608-160519618 chr1:160519608-160519617 chr1:160519606-160519619
17	POLR2A	chr1:160519045-160519457	GM12891	blood:	n/a	n/a
18	TAF1	chr1:160519065-160519492	GM12878	blood:	n/a	n/a
19	FOXM1	chr1:160519047-160519688	GM12878	blood:	n/a	n/a
20	IKZF1	chr1:160519126-160519589	GM12878	blood:	n/a	n/a
21	BATF	chr1:160519119-160519537	GM12878	blood:	n/a	n/a
22	SMC3	chr1:160519144-160519608	GM12878	blood:	n/a	n/a
23	MTA3	chr1:160517014-160521352	GM12878	blood:	n/a	n/a
24	PAX5	chr1:160519066-160519545	GM12878	blood:	n/a	n/a
25	SPI1	chr1:160519213-160519575	GM12891	blood:	n/a	chr1:160519463-160519476
26	YY1	chr1:160519081-160519502	GM12878	blood:	n/a	n/a
27	RUNX3	chr1:160518936-160519717	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:160519104-160519556	GM12878	blood:	n/a	n/a
29	RAD21	chr1:160519096-160519516	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:160518630-160519867	GM12878	blood:	n/a	n/a
31	SP1	chr1:160519052-160519572	GM12878	blood:	n/a	n/a
32	TCF3	chr1:160518844-160519538	GM12878	blood:	n/a	n/a
33	RUNX3	chr1:160518789-160519686	GM12878	blood:	n/a	n/a
34	ATF2	chr1:160518920-160519767	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:160517210-160520130	GM12892	blood:	n/a	n/a
36	PAX5	chr1:160519165-160519477	GM12891	blood:	n/a	n/a
37	IRF4	chr1:160519083-160519597	GM12878	blood:	n/a	n/a
38	WRNIP1	chr1:160519176-160519696	GM12878	blood:	n/a	n/a
39	PML	chr1:160519123-160519476	GM12878	blood:	n/a	n/a
40	EP300	chr1:160519161-160519608	GM12878	blood:	n/a	n/a
41	PAX5	chr1:160519165-160519435	GM12878	blood:	n/a	n/a
42	BCL3	chr1:160519166-160519711	GM12878	blood:	n/a	n/a
43	CEBPB	chr1:160518816-160519652	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:160518589-160519555	GM12892	blood:	n/a	n/a
45	RELA	chr1:160519032-160519816	GM19193	blood:	n/a	n/a
46	MTA3	chr1:160518798-160519876	GM12878	blood:	n/a	n/a
47	RELA	chr1:160519074-160519601	GM18951	blood:	n/a	n/a
48	RELA	chr1:160517886-160519616	GM19099	blood:	n/a	n/a
49	SPI1	chr1:160519262-160519589	GM12878	blood:	n/a	chr1:160519463-160519476
50	TCF12	chr1:160519137-160519529	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160509002..160516145-chr1:160518936..160522666,8	K562	blood:
2	chr1:160512749..160514411-chr1:160517528..160520237,2	MCF-7	breast:

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

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1055880	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11265452	0.96[CEU][hapmap]
rs11577695	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11583402	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11585738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590035	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12728784	0.81[CEU][hapmap]
rs1394078	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs151607	0.88[CEU][hapmap]
rs16832283	0.96[CEU][hapmap]
rs17381453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17385337	0.92[CEU][hapmap]
rs17385407	1.00[CEU][hapmap]
rs17385878	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1809963	0.96[CEU][hapmap]
rs2083128	0.84[CEU][hapmap]
rs2099604	0.82[CEU][hapmap]
rs2753260	0.88[CEU][hapmap]
rs3733264	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]
rs3733265	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]
rs3733266	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3755898	0.84[EUR][1000 genomes]
rs3766384	0.84[EUR][1000 genomes]
rs3766387	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs3766388	0.92[CEU][hapmap]
rs3766389	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3816146	0.84[CEU][hapmap]
rs4145897	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5002947	0.96[CEU][hapmap]
rs56040770	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61801562	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61801564	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61801565	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61801567	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802603	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61802604	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61802605	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61802606	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61802608	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802610	0.94[ASN][1000 genomes]
rs6662093	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6668760	0.81[CEU][hapmap]
rs6670721	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6687641	0.88[CEU][hapmap]
rs6692382	0.81[CEU][hapmap]
rs6697596	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6699346	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67197441	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72708818	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72708832	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7418241	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539982	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7547054	0.84[CEU][hapmap]
rs7550771	0.88[CEU][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3766385	CD84	Cis_1M	lymphoblastoid	RTeQTL
rs3766385	CD84	cis	multi-tissue	Pritchard

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	chr1:160511800-160522400	Weak transcription	Gastric	stomach
3	chr1:160511800-160527800	Weak transcription	Colonic Mucosa	Colon
4	chr1:160512200-160524600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:160514400-160519800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:160515200-160520600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:160515200-160521800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:160516000-160520600	Genic enhancers	Fetal Thymus	thymus
9	chr1:160516000-160526200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:160516200-160523800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:160516400-160520000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:160516600-160520400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:160516600-160523800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:160516800-160520600	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:160517000-160520600	Enhancers	Spleen	Spleen
16	chr1:160517400-160523800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:160517400-160524000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:160517400-160528000	Weak transcription	Placenta	Placenta
19	chr1:160517600-160519600	Genic enhancers	Monocytes-CD14+_RO01746	blood
20	chr1:160517600-160523800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:160517600-160528400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:160517800-160520200	Weak transcription	Dnd41	blood
23	chr1:160517800-160524000	Weak transcription	Adipose Nuclei	Adipose
24	chr1:160518000-160520400	Enhancers	Primary B cells from cord blood	blood
25	chr1:160518000-160520400	Enhancers	Primary B cells from peripheral blood	blood
26	chr1:160518000-160520800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:160518400-160519800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:160518600-160519600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr1:160518800-160519600	Enhancers	Fetal Brain Female	brain
30	chr1:160518800-160519600	Flanking Active TSS	GM12878-XiMat	blood
31	chr1:160518800-160519800	Enhancers	Duodenum Mucosa	Duodenum
32	chr1:160519200-160519600	Strong transcription	Primary T cells from cord blood	blood
33	chr1:160519200-160519600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:160519200-160521200	Enhancers	Pancreas	Pancrea
35	chr1:160519200-160521400	Enhancers	K562	blood
36	chr1:160519200-160521600	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr1:160519200-160522200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:160519200-160524000	Strong transcription	Primary hematopoietic stem cells	blood
39	chr1:160519400-160520400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:160519400-160521200	Genic enhancers	Thymus	Thymus
41	chr1:160519400-160521800	Weak transcription	Stomach Mucosa	stomach
42	chr1:160519400-160524200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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