Variant report

Variant	rs1144396
Chromosome Location	chr11:102679052-102679053
allele	A/C
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	RAD21	chr11:102678655-102679139	A549	lung:	n/a	chr11:102679032-102679041 chr11:102678704-102678717 chr11:102678986-102679000
2	CTCF	chr11:102678728-102679063	GM12878	blood:	n/a	n/a
3	RAD21	chr11:102678689-102679138	ECC-1	luminal epithelium:	n/a	chr11:102679032-102679041 chr11:102678704-102678717 chr11:102678986-102679000
4	CTCF	chr11:102678708-102679075	A549	lung:	n/a	n/a
5	CTCF	chr11:102679000-102679150	HFF-Myc	foreskin:	n/a	n/a
6	CTCF	chr11:102678980-102679130	GM12864	blood:	n/a	n/a
7	TEAD4	chr11:102678682-102679095	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr11:102678743-102679101	K562	blood:	n/a	n/a
9	RAD21	chr11:102678733-102679058	HepG2	liver:	n/a	chr11:102679032-102679041 chr11:102678986-102679000
10	YY1	chr11:102678680-102679090	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr11:102678701-102679096	H1-hESC	embryonic stem cell:	n/a	chr11:102679032-102679041 chr11:102678704-102678717 chr11:102678986-102679000
12	SMC3	chr11:102678732-102679076	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr11:102678739-102679053	A549	lung:	n/a	n/a
14	MAX	chr11:102678576-102679099	H1-hESC	embryonic stem cell:	n/a	n/a
15	YY1	chr11:102678691-102679160	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr11:102678739-102679058	IMR90	lung:	n/a	n/a
17	RAD21	chr11:102678616-102679115	H1-hESC	embryonic stem cell:	n/a	chr11:102679032-102679041 chr11:102678704-102678717 chr11:102678986-102679000
18	CTCF	chr11:102678712-102679083	MCF-7	breast:	n/a	n/a
19	CTCF	chr11:102678940-102679090	WI-38	lung:	n/a	n/a
20	CHD2	chr11:102678753-102679112	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr11:102678735-102679073	HepG2	liver:	n/a	chr11:102679032-102679041 chr11:102678986-102679000
22	RAD21	chr11:102678613-102679060	H1-hESC	embryonic stem cell:	n/a	chr11:102679032-102679041 chr11:102678704-102678717 chr11:102678986-102679000
23	NRF1	chr11:102678760-102679056	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr11:102678512-102679107	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr11:102678600-102679137	MCF-7	breast:	n/a	n/a
26	FOXA1	chr11:102678664-102679059	T-47D	breast:	n/a	n/a
27	CREB1	chr11:102678586-102679083	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr11:102678582-102679207	A549	lung:	n/a	n/a
29	CTCF	chr11:102678704-102679081	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr11:102678640-102679075	HCT-116	colon:	n/a	n/a
31	POLR2A	chr11:102679012-102679197	MCF10A-Er-Src	breast:	n/a	n/a
32	RAD21	chr11:102678728-102679096	Hela-S3	cervix:	n/a	chr11:102679032-102679041 chr11:102678986-102679000
33	CTCF	chr11:102678544-102679288	SK-N-SH	brain:	n/a	n/a
34	RAD21	chr11:102678704-102679115	A549	lung:	n/a	chr11:102679032-102679041 chr11:102678704-102678717 chr11:102678986-102679000
35	CTCF	chr11:102678737-102679052	MCF-7	breast:	n/a	n/a
36	TBP	chr11:102678591-102679083	H1-hESC	embryonic stem cell:	n/a	chr11:102678690-102678701
37	ZNF143	chr11:102678380-102679082	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr11:102678635-102679104	H1-hESC	embryonic stem cell:	n/a	n/a
39	GABPA	chr11:102678580-102679059	K562	blood:	n/a	n/a
40	POLR2A	chr11:102678666-102679089	HCT-116	colon:	n/a	n/a
41	RAD21	chr11:102678706-102679069	HepG2	liver:	n/a	chr11:102679032-102679041 chr11:102678986-102679000
42	CTCF	chr11:102678743-102679054	MCF-7	breast:	n/a	n/a
43	CTCF	chr11:102678677-102679074	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000256035	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1010698	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10791596	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895364	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895365	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10895366	0.85[EUR][1000 genomes]
rs11225434	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1144397	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs12792871	0.85[EUR][1000 genomes]
rs12801529	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12804136	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2097248	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2155013	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2212637	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4754884	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs484915	0.82[JPT][hapmap];0.81[MEX][hapmap]
rs502174	0.95[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs520540	0.95[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs526215	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs565082	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs573521	0.81[ASN][1000 genomes]
rs575027	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs591058	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs595840	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs602128	0.94[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs617819	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs632478	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs633962	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs635746	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs639752	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs645419	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6590993	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6590994	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs666734	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs678815	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs679620	0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7117013	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7118731	0.95[ASN][1000 genomes]
rs7126392	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs756544	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7926920	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7946057	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1144396	TMEM123	cis	lymphoblastoid	seeQTL
rs1144396	GRIA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102678400-102679200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:102678600-102679200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr11:102678600-102679200	Active TSS	A549	lung
4	chr11:102678800-102690000	Weak transcription	Gastric	stomach
5	chr11:102679000-102679200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr11:102679000-102690400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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