Variant report

Variant	rs3766074
Chromosome Location	chr1:169163017-169163018
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	CTCF	chr1:169162780-169163038	K562	blood:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
2	CTCF	chr1:169162880-169163030	NHLF	lung:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
3	CBX3	chr1:169162657-169163091	K562	blood:	n/a	n/a
4	ZMIZ1	chr1:169162694-169163037	K562	blood:	n/a	n/a
5	CTCF	chr1:169162743-169163035	SK-N-SH_RA	brain:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
6	RAD21	chr1:169162727-169163078	SK-N-SH_RA	brain:	n/a	chr1:169162918-169162932 chr1:169162914-169162933
7	CEBPB	chr1:169162641-169163058	K562	blood:	n/a	chr1:169162899-169162912
8	TAL1	chr1:169162636-169163111	K562	blood:	n/a	chr1:169162853-169162871 chr1:169162920-169162929
9	RCOR1	chr1:169162676-169163079	K562	blood:	n/a	n/a
10	CEBPB	chr1:169162747-169163030	K562	blood:	n/a	chr1:169162899-169162912
11	STAT5A	chr1:169162587-169163122	K562	blood:	n/a	n/a
12	MYC	chr1:169162666-169163083	K562	blood:	n/a	chr1:169162873-169162883 chr1:169162848-169162858
13	JUND	chr1:169162700-169163061	K562	blood:	n/a	chr1:169163003-169163012
14	MAX	chr1:169162692-169163076	K562	blood:	n/a	chr1:169162873-169162883 chr1:169162848-169162858
15	CTCF	chr1:169162920-169163070	HCM	heart:	n/a	n/a
16	RAD21	chr1:169162732-169163028	K562	blood:	n/a	chr1:169162918-169162932 chr1:169162914-169162933
17	SMC3	chr1:169162425-169163239	SK-N-SH	brain:	n/a	chr1:169162925-169162932
18	RCOR1	chr1:169162589-169163088	K562	blood:	n/a	n/a
19	MAZ	chr1:169162779-169163105	K562	blood:	n/a	n/a
20	TRIM28	chr1:169162656-169163144	K562	blood:	n/a	n/a
21	EP300	chr1:169162652-169163081	K562	blood:	n/a	chr1:169162897-169162911
22	ZNF143	chr1:169162777-169163026	K562	blood:	n/a	n/a
23	CEBPB	chr1:169162689-169163094	K562	blood:	n/a	chr1:169162899-169162912
24	HDAC2	chr1:169162652-169163052	K562	blood:	n/a	chr1:169162863-169162872
25	CTCF	chr1:169162880-169163030	HRPEpiC	eye:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
26	CUX1	chr1:169162746-169163031	K562	blood:	n/a	n/a
27	GATA2	chr1:169162753-169163019	K562	blood:	n/a	chr1:169162853-169162870 chr1:169162864-169162874 chr1:169162862-169162872 chr1:169162862-169162871 chr1:169162864-169162871
28	CTCF	chr1:169162812-169163082	K562	blood:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
29	MXI1	chr1:169162230-169163290	SK-N-SH	brain:	n/a	n/a
30	PML	chr1:169162571-169163081	K562	blood:	n/a	n/a
31	CTCF	chr1:169162855-169163054	IMR90	lung:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
32	MAX	chr1:169162773-169163030	NB4	blood:	n/a	chr1:169162873-169162883 chr1:169162848-169162858
33	RAD21	chr1:169162453-169163318	SK-N-SH	brain:	n/a	chr1:169162918-169162932 chr1:169162914-169162933
34	CTCF	chr1:169162880-169163030	SK-N-SH_RA	brain:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
35	ARID3A	chr1:169162810-169163064	K562	blood:	n/a	n/a
36	CTCF	chr1:169162900-169163050	HPF	lung:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
37	PML	chr1:169162605-169163047	K562	blood:	n/a	n/a
38	CTCF	chr1:169162920-169163070	BE2_C	brain:	n/a	n/a
39	CTCF	chr1:169162880-169163030	HCPEpiC	choroid plexus:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
40	GATA1	chr1:169162394-169163897	PBDE	blood:	n/a	chr1:169162853-169162870 chr1:169162864-169162874 chr1:169162862-169162872 chr1:169162862-169162871 chr1:169162864-169162871
41	TEAD4	chr1:169162587-169163114	K562	blood:	n/a	n/a
42	GABPA	chr1:169162757-169163066	K562	blood:	n/a	n/a
43	CEBPD	chr1:169162605-169163142	K562	blood:	n/a	n/a
44	GATA2	chr1:169162631-169163090	SH-SY5Y	brain:	n/a	chr1:169162853-169162870 chr1:169162864-169162874 chr1:169162862-169162872 chr1:169162862-169162871 chr1:169162864-169162871
45	CTCF	chr1:169162709-169163132	SK-N-SH	brain:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
46	RAD21	chr1:169162675-169163048	SK-N-SH_RA	brain:	n/a	chr1:169162918-169162932 chr1:169162914-169162933
47	TBL1XR1	chr1:169162719-169163089	K562	blood:	n/a	n/a
48	CTCF	chr1:169162731-169163136	K562	blood:	n/a	chr1:169162918-169162931 chr1:169162916-169162934
49	STAT5A	chr1:169162665-169163075	K562	blood:	n/a	n/a
50	CTCF	chr1:169162880-169163030	HPAF	blood vessel:	n/a	chr1:169162918-169162931 chr1:169162916-169162934

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169162826..169163552-chr6:14536621..14537302,2	MCF-7	breast:

Variant related genes	Relation type
NME7	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1011638	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1018832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10458388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10458394	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10489417	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10494477	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10494478	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10800429	1.00[JPT][hapmap]
rs10800431	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10800432	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10800433	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919062	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.85[ASN][1000 genomes]
rs10919070	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10919071	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10919074	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10919085	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919087	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919125	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919128	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919144	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10919147	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs10919158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs12021696	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12022617	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12025566	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12029800	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12029857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030541	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12030810	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12031371	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12035622	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12036426	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12042082	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12042990	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12045803	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12048188	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12401966	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403181	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12405725	0.85[JPT][hapmap]
rs12406341	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12408636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12410241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12410387	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12410456	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12410548	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567342	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12568473	0.85[ASN][1000 genomes]
rs17345156	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17345426	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2000321	0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2001155	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001156	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2143290	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34323371	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4497270	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4562680	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72706963	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72706975	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7413522	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7528142	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7556463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3766074	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
2	chr1:169161800-169163800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:169162200-169163600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:169162200-169163600	Enhancers	Ovary	ovary
5	chr1:169162400-169163600	Enhancers	Fetal Heart	heart
6	chr1:169162600-169163600	Enhancers	Psoas Muscle	Psoas
7	chr1:169162800-169163400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:169162800-169167600	Weak transcription	Fetal Lung	lung
9	chr1:169163000-169165000	Weak transcription	Primary hematopoietic stem cells	blood

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