Variant report

Variant	rs4506675
Chromosome Location	chr11:60101593-60101594
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	CTCF	chr11:60101561-60101807	MCF-7	breast:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
2	RAD21	chr11:60101515-60101875	H1-hESC	embryonic stem cell:	n/a	chr11:60101692-60101711
3	CTCF	chr11:60101455-60101840	HepG2	liver:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
4	CTCF	chr11:60101537-60101838	Spleen_OC	spleen:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
5	CTCF	chr11:60101525-60101797	GM19239	blood:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
6	FOS	chr11:60101505-60101760	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr11:60101580-60101769	MCF-7	breast:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
8	CTCF	chr11:60101426-60101892	K562	blood:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
9	RAD21	chr11:60101519-60101883	GM12878	blood:	n/a	chr11:60101692-60101711
10	YY1	chr11:60101347-60101763	GM12892	blood:	n/a	chr11:60101615-60101627 chr11:60101619-60101627
11	CTCF	chr11:60101572-60101793	GM20000	blood:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
12	RAD21	chr11:60101497-60101802	GM12878	blood:	n/a	chr11:60101692-60101711
13	TCF7L2	chr11:60101558-60101807	PANC-1	pancreas:	n/a	chr11:60101637-60101647
14	CTCF	chr11:60101514-60101806	GM19240	blood:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
15	YY1	chr11:60101552-60101769	K562	blood:	n/a	chr11:60101615-60101627 chr11:60101619-60101627
16	YY1	chr11:60101457-60101794	HCT-116	colon:	n/a	chr11:60101615-60101627 chr11:60101619-60101627
17	ZNF143	chr11:60101520-60101869	GM12878	blood:	n/a	n/a
18	CTCF	chr11:60101381-60101999	HCT-116	colon:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
19	CTCF	chr11:60101562-60101766	MCF-7	breast:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
20	CEBPB	chr11:60101539-60101743	HepG2	liver:	n/a	n/a
21	RAD21	chr11:60101477-60102001	HCT-116	colon:	n/a	chr11:60101692-60101711
22	CTCF	chr11:60101588-60101797	GM10248	blood:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
23	SMC3	chr11:60101376-60101937	SK-N-SH	brain:	n/a	chr11:60101693-60101707
24	CTCF	chr11:60101576-60101806	Kidney_OC	kidney:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
25	CTCF	chr11:60101536-60101830	T-47D	breast:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
26	FOS	chr11:60101473-60101836	MCF10A-Er-Src	breast:	n/a	n/a
27	CTCF	chr11:60101580-60101730	NHEK	skin:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
28	CTCF	chr11:60101551-60101800	A549	lung:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
29	CTCF	chr11:60101540-60101795	ECC-1	luminal epithelium:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
30	CTCF	chr11:60101536-60102005	HCT-116	colon:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
31	CTCF	chr11:60101560-60101710	AG09309	skin:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
32	CTCF	chr11:60101546-60101799	HepG2	liver:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
33	FOSL2	chr11:60101447-60101760	HepG2	liver:	n/a	n/a
34	CTCF	chr11:60101500-60101885	K562	blood:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
35	TCF7L2	chr11:60101457-60101793	Hela-S3	cervix:	n/a	chr11:60101637-60101647
36	CTCF	chr11:60101489-60101837	K562	blood:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
37	CTCF	chr11:60101547-60101820	GM10266	blood:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
38	CTCF	chr11:60101431-60101851	MCF-7	breast:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
39	CTCF	chr11:60101580-60101811	Hela-S3	cervix:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
40	CTCF	chr11:60101587-60101815	Lung_OC	lung:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
41	CTCF	chr11:60101554-60101799	Fibrobl	skin:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
42	RAD21	chr11:60101522-60101871	H1-hESC	embryonic stem cell:	n/a	chr11:60101692-60101711
43	RFX5	chr11:60101457-60101594	HepG2	liver:	n/a	n/a
44	CTCF	chr11:60101581-60101796	Pancreas_OC	pancreas:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
45	RAD21	chr11:60101399-60102013	SK-N-SH	brain:	n/a	chr11:60101692-60101711
46	MAZ	chr11:60101561-60101708	HepG2	liver:	n/a	n/a
47	CTCF	chr11:60101580-60101730	HMF	breast:	n/a	chr11:60101696-60101706 chr11:60101691-60101709
48	CTCF	chr11:60101540-60101690	GM12866	blood:	n/a	n/a
49	MYC	chr11:60101543-60101829	NB4	blood:	n/a	n/a
50	JUND	chr11:60101487-60101674	H1-hESC	embryonic stem cell:	n/a	chr11:60101592-60101603

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:60101561-60101611	BJ	skin:	n/a
2	chr11:60101561-60101611	RPTEC	kidney:	n/a
3	chr11:60101561-60101611	HL-60	blood:	n/a
4	chr11:60101561-60101611	T-47D	breast:	n/a
5	chr11:60101561-60101611	HRPEpiC	eye:	n/a
6	chr11:60101561-60101611	AG04450	lung:	fetal
7	chr11:60101561-60101611	MCF10A-Er-Src	breast:	n/a
8	chr11:60101561-60101611	AG10803	skin:	n/a
9	chr11:60101561-60101611	IMR90	lung:	fetal
10	chr11:60101561-60101611	HRCEpiC	kidney:	n/a
11	chr11:60101561-60101611	GM19239	blood:	n/a
12	chr11:60101561-60101611	HEEpiC	esophagus:	n/a
13	chr11:60101561-60101611	NHDF-neo	bronchial:	n/a
14	chr11:60101561-60101611	Hela-S3	cervix:	n/a
15	chr11:60101561-60101611	GM06990	blood:	n/a
16	chr11:60101561-60101611	PFSK-1	brain:	n/a
17	chr11:60101561-60101611	Jurkat	blood:	n/a
18	chr11:60101561-60101611	GM12892	blood:	n/a
19	chr11:60101561-60101611	MCF-7	breast:	n/a
20	chr11:60101561-60101611	U87	brain:	n/a
21	chr11:60101561-60101611	AG09309	skin:	n/a
22	chr11:60101561-60101611	PANC-1	pancreas:	n/a
23	chr11:60101561-60101611	HIPEpiC	eye:	n/a
24	chr11:60101561-60101611	ovcar-3	ovarian:	n/a
25	chr11:60101561-60101611	Hepatocyte	liver:	n/a
26	chr11:60101561-60101611	BE2_C	brain:	n/a
27	chr11:60101561-60101611	CMK	blood:	n/a
28	chr11:60101561-60101611	AoSMC	blood vessel:	n/a
29	chr11:60101561-60101611	AG09319	gingival:	n/a
30	chr11:60101561-60101611	GM12891	blood:	n/a
31	chr11:60101561-60101611	HMEC	breast:	n/a
32	chr11:60101561-60101611	HRE	kidney:	n/a
33	chr11:60101561-60101611	PrEC	prostate:	n/a
34	chr11:60101561-60101611	HCF	heart:	n/a
35	chr11:60101561-60101611	HCPEpiC	choroid plexus:	n/a
36	chr11:60101561-60101611	ProgFib	skin:	n/a
37	chr11:60101561-60101611	NH-A	brain:	n/a
38	chr11:60101561-60101611	SKMC	muscle:	n/a
39	chr11:60101561-60101611	GM12878	blood:	n/a
40	chr11:60101561-60101611	LNCaP	prostate:	n/a
41	chr11:60101561-60101611	HepG2	liver:	n/a
42	chr11:60101561-60101611	Caco-2	colon:	n/a
43	chr11:60101561-60101611	H1-hESC	embryonic stem cell:	embryo
44	chr11:60101561-60101611	HCT-116	colon:	n/a
45	chr11:60101561-60101611	HAEpiC	amniotic membrane:	n/a
46	chr11:60101561-60101611	NB4	blood:	n/a
47	chr11:60101561-60101611	SK-N-SH	brain:	n/a
48	chr11:60101561-60101611	A549	lung:	n/a
49	chr11:60101561-60101611	HUVEC	blood vessel:	n/a
50	chr11:60101561-60101611	NHBE	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:60100804..60102100-chr11:60385189..60386876,4	MCF-7	breast:
2	chr11:60101406..60101985-chr11:60253130..60254013,3	MCF-7	breast:
3	chr11:60032789..60033679-chr11:60101235..60102123,2	MCF-7	breast:

Variant related genes	Relation type
MS4A6E	TF binding region
MS4A6E	CpG island

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1020288	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10431136	0.81[CEU][hapmap]
rs10750932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750933	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10750934	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792264	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792267	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792268	0.80[ASW][hapmap];0.83[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[EUR][1000 genomes]
rs10897027	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10897028	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10897030	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10897031	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10897032	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10897033	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10897044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10897045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10897046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10897047	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897048	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897049	0.80[ASW][hapmap];0.83[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[EUR][1000 genomes]
rs11230239	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs11230240	0.83[CEU][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs11230243	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11230248	0.86[EUR][1000 genomes]
rs11230275	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11230276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11230280	0.86[EUR][1000 genomes]
rs11605188	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605235	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12225299	0.86[EUR][1000 genomes]
rs12792791	0.84[EUR][1000 genomes]
rs12798157	0.86[EUR][1000 genomes]
rs12802385	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1443250	0.81[MEX][hapmap];0.85[EUR][1000 genomes]
rs1899571	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1899572	0.84[EUR][1000 genomes]
rs2289614	0.83[CEU][hapmap]
rs2304933	0.80[ASW][hapmap];0.83[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[EUR][1000 genomes]
rs2304934	0.83[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs2304935	0.80[ASW][hapmap];0.83[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.86[EUR][1000 genomes]
rs2304936	0.86[EUR][1000 genomes]
rs2868118	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2868119	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2868120	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2868121	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35905922	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4477457	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61900468	0.85[EUR][1000 genomes]
rs7103808	0.84[EUR][1000 genomes]
rs7108879	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7116069	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7931525	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs7950431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4506675	ZP1	cis	parietal	SCAN
rs4506675	HNRNPUL2	cis	parietal	SCAN
rs4506675	HRASLS2	cis	parietal	SCAN
rs4506675	MS4A4A	cis	cerebellum	SCAN
rs4506675	OR8J1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:60099800-60101800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr11:60100800-60104400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:60101000-60104200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:60101000-60105400	Enhancers	Placenta	Placenta
5	chr11:60101200-60101800	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr11:60101200-60104000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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