Variant report

Variant	rs2712228
Chromosome Location	chr7:107300340-107300341
allele	G/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	JUN	chr7:107300141-107300421	K562	blood:	n/a	n/a
2	ATF1	chr7:107300192-107300470	K562	blood:	n/a	n/a
3	JUND	chr7:107300073-107300540	K562	blood:	n/a	n/a
4	TBL1XR1	chr7:107300132-107300437	K562	blood:	n/a	n/a
5	JUND	chr7:107299959-107300545	HCT-116	colon:	n/a	n/a
6	E2F4	chr7:107300173-107300470	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr7:107300110-107300483	Hela-S3	cervix:	n/a	n/a
8	PML	chr7:107299999-107300479	K562	blood:	n/a	n/a
9	STAT5A	chr7:107300052-107300497	K562	blood:	n/a	chr7:107300351-107300366
10	JUN	chr7:107299220-107301021	K562	blood:	n/a	chr7:107300858-107300870
11	TCF7L2	chr7:107300025-107300452	HCT-116	colon:	n/a	n/a
12	FOSL1	chr7:107299954-107300546	HCT-116	colon:	n/a	n/a
13	MYC	chr7:107300167-107300368	NB4	blood:	n/a	chr7:107300285-107300295
14	STAT5A	chr7:107300107-107300582	K562	blood:	n/a	chr7:107300351-107300366
15	BHLHE40	chr7:107300195-107300511	K562	blood:	n/a	n/a
16	MAX	chr7:107300161-107300591	K562	blood:	n/a	chr7:107300285-107300295
17	MYC	chr7:107300129-107300424	MCF10A-Er-Src	breast:	n/a	chr7:107300285-107300295
18	MAZ	chr7:107300219-107300398	K562	blood:	n/a	n/a
19	FOS	chr7:107300076-107300575	MCF10A-Er-Src	breast:	n/a	chr7:107300260-107300271
20	CEBPB	chr7:107299999-107300587	HCT-116	colon:	n/a	n/a
21	CEBPB	chr7:107300143-107300467	K562	blood:	n/a	n/a
22	STAT3	chr7:107300008-107300711	MCF10A-Er-Src	breast:	n/a	chr7:107300348-107300369
23	CEBPB	chr7:107299981-107300523	HCT-116	colon:	n/a	n/a
24	MAX	chr7:107300180-107300452	NB4	blood:	n/a	chr7:107300285-107300295
25	MAFK	chr7:107300140-107300427	IMR90	lung:	n/a	n/a
26	CEBPB	chr7:107300065-107300863	IMR90	lung:	n/a	chr7:107300729-107300742 chr7:107300730-107300741 chr7:107300729-107300740
27	TEAD4	chr7:107299842-107300703	K562	blood:	n/a	n/a
28	FOS	chr7:107300092-107300485	MCF10A-Er-Src	breast:	n/a	chr7:107300260-107300271
29	FOS	chr7:107299941-107300514	MCF10A-Er-Src	breast:	n/a	chr7:107300260-107300271
30	POU2F2	chr7:107300196-107300452	GM12891	blood:	n/a	n/a
31	EBF1	chr7:107300253-107300398	GM12878	blood:	n/a	chr7:107300327-107300338
32	CEBPB	chr7:107300110-107300468	K562	blood:	n/a	n/a
33	STAT3	chr7:107300094-107300515	MCF10A-Er-Src	breast:	n/a	chr7:107300348-107300369
34	STAT3	chr7:107300093-107300538	MCF10A-Er-Src	breast:	n/a	chr7:107300348-107300369
35	CEBPB	chr7:107300100-107300798	Hela-S3	cervix:	n/a	chr7:107300729-107300742 chr7:107300730-107300741 chr7:107300729-107300740
36	MYC	chr7:107300080-107300552	K562	blood:	n/a	chr7:107300285-107300295
37	E2F6	chr7:107300203-107300409	K562	blood:	n/a	n/a
38	MAX	chr7:107300200-107300444	K562	blood:	n/a	chr7:107300285-107300295
39	FOS	chr7:107300073-107300486	HUVEC	blood vessel:	n/a	chr7:107300260-107300271
40	RCOR1	chr7:107299956-107300628	K562	blood:	n/a	n/a
41	MAFK	chr7:107300200-107300432	K562	blood:	n/a	n/a
42	POLR2A	chr7:107300112-107300426	SK-N-SH	brain:	n/a	n/a
43	EP300	chr7:107299988-107300536	K562	blood:	n/a	n/a
44	MYC	chr7:107300132-107300470	MCF10A-Er-Src	breast:	n/a	chr7:107300285-107300295
45	MAX	chr7:107300118-107300537	K562	blood:	n/a	chr7:107300285-107300295
46	MAX	chr7:107299988-107300587	HCT-116	colon:	n/a	chr7:107300285-107300295
47	MAX	chr7:107300180-107300423	Hela-S3	cervix:	n/a	chr7:107300285-107300295
48	STAT3	chr7:107300178-107300438	Hela-S3	cervix:	n/a	chr7:107300348-107300369
49	ATF3	chr7:107300052-107300458	K562	blood:	n/a	n/a
50	STAT3	chr7:107300109-107300427	MCF10A-Er-Src	breast:	n/a	chr7:107300348-107300369

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COG5-1	chr7:107297075-107300651	ENSG00000233705
2	lnc-COG5-1	chr7:107300179-107300651	NONHSAT122699
3	lnc-COG5-1	chr7:107296961-107300651	NONHSAT122700
4	lnc-COG5-1	chr7:107300179-107300651	NONHSAT122701

Variant related genes	Relation type
SLC26A4	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1015411	0.87[CEU][hapmap]
rs10237948	0.82[EUR][1000 genomes]
rs10258385	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10267907	0.86[CEU][hapmap]
rs10273733	0.91[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs10274041	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs10276604	0.91[CEU][hapmap]
rs10281535	0.91[CEU][hapmap]
rs11771278	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11977187	0.91[CEU][hapmap]
rs12673675	0.87[CEU][hapmap]
rs13228252	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2057837	0.91[CEU][hapmap]
rs2066735	0.87[CEU][hapmap]
rs2107713	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2178497	0.91[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2237677	0.87[CEU][hapmap]
rs2248465	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2253146	0.87[CEU][hapmap]
rs2253269	0.82[CEU][hapmap]
rs2253271	0.86[CEU][hapmap]
rs2293658	0.87[EUR][1000 genomes]
rs2395907	0.91[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs2520241	0.87[CEU][hapmap]
rs2520242	0.87[CEU][hapmap]
rs2520243	0.82[CEU][hapmap]
rs2520245	0.82[CEU][hapmap]
rs2520249	0.87[CEU][hapmap]
rs2520268	0.91[CEU][hapmap]
rs2520269	0.82[CEU][hapmap]
rs2701678	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2701679	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2701684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701685	1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2701687	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs2712201	0.87[CEU][hapmap]
rs2712227	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2712229	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808	0.91[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs2894466	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2894475	0.91[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs3094383	0.86[CEU][hapmap]
rs3779494	0.84[EUR][1000 genomes]
rs3801944	0.91[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs3801948	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4727684	0.91[CEU][hapmap]
rs6976607	0.91[CEU][hapmap]
rs7778250	0.91[CEU][hapmap]
rs7778270	0.91[CEU][hapmap]
rs7793613	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7803102	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs986994	0.87[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2712228	BCAP29	Cis_1M	lymphoblastoid	RTeQTL
rs2712228	COG5	cis	parietal	SCAN
rs2712228	COG5	cis	cerebellum	SCAN
rs2712228	LAP3	trans	cerebellum	SCAN
rs2712228	NRCAM	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107298600-107300800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:107299200-107301200	Bivalent/Poised TSS	Fetal Brain Female	brain
3	chr7:107299400-107301800	Enhancers	Dnd41	blood
4	chr7:107299600-107300600	Enhancers	Osteobl	bone
5	chr7:107299800-107300400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr7:107299800-107301000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:107299800-107301200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:107299800-107301200	Enhancers	K562	blood
9	chr7:107300000-107300400	Bivalent Enhancer	NHDF-Ad	bronchial
10	chr7:107300000-107300600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:107300000-107300600	Enhancers	Primary B cells from peripheral blood	blood
12	chr7:107300000-107300800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:107300000-107300800	Bivalent Enhancer	GM12878-XiMat	blood
14	chr7:107300000-107300800	Enhancers	NH-A	brain
15	chr7:107300000-107301200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:107300000-107301200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:107300200-107300400	Enhancers	HUVEC	blood vessel
18	chr7:107300200-107300800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr7:107300200-107301000	Bivalent Enhancer	Primary B cells from cord blood	blood
20	chr7:107300200-107301000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr7:107300200-107301000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr7:107300200-107301200	Bivalent Enhancer	Primary T cells from cord blood	blood
23	chr7:107300200-107301400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:107300200-107301600	Bivalent Enhancer	Fetal Thymus	thymus

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