Variant report

Variant	rs12899940
Chromosome Location	chr15:79001699-79001700
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	RAD21	chr15:79001579-79002178	ECC-1	luminal epithelium:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
2	CTCF	chr15:79001517-79002135	HCT-116	colon:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
3	CTCF	chr15:79001603-79002042	MCF-7	breast:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
4	RAD21	chr15:79001694-79002026	K562	blood:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
5	MAZ	chr15:79001684-79002058	K562	blood:	n/a	n/a
6	RAD21	chr15:79001625-79002195	H1-hESC	embryonic stem cell:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
7	CTCF	chr15:79001279-79002507	A549	lung:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
8	SMC3	chr15:79000991-79002566	SK-N-SH	brain:	n/a	chr15:79001916-79001930
9	RAD21	chr15:79001468-79002278	HCT-116	colon:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
10	RAD21	chr15:79000804-79002555	SK-N-SH	brain:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
11	MXI1	chr15:79000695-79002216	SK-N-SH	brain:	n/a	n/a
12	RAD21	chr15:79001609-79002114	SK-N-SH_RA	brain:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
13	SMC3	chr15:79001638-79002137	Hela-S3	cervix:	n/a	chr15:79001916-79001930
14	CTCF	chr15:79001630-79002228	A549	lung:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
15	RAD21	chr15:79001690-79002099	HepG2	liver:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
16	RAD21	chr15:79001601-79002127	ECC-1	luminal epithelium:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
17	RAD21	chr15:79001528-79002271	HCT-116	colon:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
18	RAD21	chr15:79001510-79002182	MCF-7	breast:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
19	ELF1	chr15:79001698-79002060	K562	blood:	n/a	n/a
20	CTCF	chr15:79001697-79002173	T-47D	breast:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
21	MAX	chr15:79001685-79002012	Hela-S3	cervix:	n/a	n/a
22	RAD21	chr15:79001572-79002144	A549	lung:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
23	CTCF	chr15:79001284-79002708	SK-N-SH	brain:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
24	RAD21	chr15:79001582-79002279	MCF-7	breast:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
25	EP300	chr15:79000386-79002398	SK-N-SH	brain:	n/a	chr15:79001742-79001756 chr15:79000930-79000937 chr15:79001048-79001062
26	RAD21	chr15:79001679-79002098	HepG2	liver:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
27	CTCF	chr15:79001694-79002127	K562	blood:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
28	RAD21	chr15:79001652-79002170	H1-hESC	embryonic stem cell:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
29	SMC3	chr15:79001544-79002103	GM12878	blood:	n/a	chr15:79001916-79001930
30	POU2F2	chr15:79001670-79002147	GM12878	blood:	n/a	chr15:79002043-79002055
31	RAD21	chr15:79001669-79002177	H1-hESC	embryonic stem cell:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
32	RAD21	chr15:79001604-79002171	HepG2	liver:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
33	CTCF	chr15:79001658-79002261	K562	blood:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
34	CTCF	chr15:79001686-79002085	SK-N-SH_RA	brain:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
35	CTCF	chr15:79001659-79002139	K562	blood:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
36	CTCF	chr15:79001687-79002127	A549	lung:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
37	MAFK	chr15:79001691-79002056	Hela-S3	cervix:	n/a	n/a
38	PAX5	chr15:79001610-79002157	GM12878	blood:	n/a	chr15:79001744-79001753
39	RAD21	chr15:79001631-79002181	IMR90	lung:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
40	RAD21	chr15:79001610-79002129	Hela-S3	cervix:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
41	RAD21	chr15:79001694-79002110	GM12878	blood:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
42	CTCF	chr15:79001665-79002133	H1-hESC	embryonic stem cell:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
43	MAZ	chr15:79001589-79002217	IMR90	lung:	n/a	n/a
44	FOXM1	chr15:79001699-79002071	GM12878	blood:	n/a	n/a
45	CTCF	chr15:79001581-79002104	MCF-7	breast:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930
46	RAD21	chr15:79001192-79002171	SK-N-SH_RA	brain:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
47	POLR2A	chr15:79001577-79001877	SK-N-SH	brain:	n/a	n/a
48	RAD21	chr15:79001688-79002051	GM12878	blood:	n/a	chr15:79001798-79001810 chr15:79001912-79001931 chr15:79001915-79001928
49	PAX5	chr15:79001699-79002095	GM12878	blood:	n/a	chr15:79001744-79001753
50	CTCF	chr15:79001575-79002191	HCT-116	colon:	n/a	chr15:79001922-79001930 chr15:79001916-79001929 chr15:79001921-79001929 chr15:79001914-79001932 chr15:79001909-79001930

No.	Distal block	Cell Line	Cell type
1	chr15:78930457..78931362-chr15:79001508..79002101,2	MCF-7	breast:
2	chr15:78910469..78911614-chr15:79001380..79002343,7	MCF-7	breast:
3	chr15:78910694..78911323-chr15:79001429..79002024,2	MCF-7	breast:
4	chr15:78910051..78911529-chr15:79000733..79002666,9	K562	blood:
5	chr15:78930812..78931988-chr15:79001204..79002352,8	MCF-7	breast:
6	chr15:78909956..78912504-chr15:79001139..79003801,2	MCF-7	breast:

Variant related genes	Relation type
CHRNB4	TF binding region
ENSG00000080644	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11072787	0.89[CEU][hapmap]
rs11072793	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072794	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072799	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11629639	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11629824	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633170	0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633519	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11634628	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852887	0.81[EUR][1000 genomes]
rs11852909	0.85[EUR][1000 genomes]
rs11856441	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12901228	0.83[EUR][1000 genomes]
rs12907178	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907511	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1383634	0.84[EUR][1000 genomes]
rs1383635	0.84[EUR][1000 genomes]
rs1809412	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1809414	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1814880	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1825086	0.84[EUR][1000 genomes]
rs1904920	0.81[EUR][1000 genomes]
rs2219939	0.84[EUR][1000 genomes]
rs4887074	0.84[CEU][hapmap]
rs4887078	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887091	0.94[CEU][hapmap]
rs6495317	0.83[ASN][1000 genomes]
rs6495318	0.84[ASN][1000 genomes]
rs7163236	0.83[ASN][1000 genomes]
rs7170552	0.84[ASN][1000 genomes]
rs7170563	0.82[ASN][1000 genomes]
rs7182567	0.95[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap]
rs72625802	0.84[ASN][1000 genomes]
rs8039600	0.83[ASN][1000 genomes]
rs8043123	0.84[CEU][hapmap]
rs899997	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9888691	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12899940	TMED3	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79001400-79001800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
2	chr15:79001400-79001800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr15:79001400-79001800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:79001400-79001800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:79001400-79001800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
6	chr15:79001400-79002000	Bivalent Enhancer	Thymus	Thymus
7	chr15:79001400-79002200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:79001400-79002200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr15:79001400-79002200	Bivalent Enhancer	Fetal Thymus	thymus
10	chr15:79001600-79001800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
11	chr15:79001600-79001800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr15:79001600-79001800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr15:79001600-79001800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:79001600-79001800	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:79001600-79001800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
16	chr15:79001600-79001800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
17	chr15:79001600-79001800	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr15:79001600-79001800	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr15:79001600-79001800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:79001600-79001800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:79001600-79001800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
22	chr15:79001600-79001800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:79001600-79001800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:79001600-79001800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:79001600-79001800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
26	chr15:79001600-79001800	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr15:79001600-79001800	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr15:79001600-79001800	Bivalent/Poised TSS	Fetal Lung	lung
29	chr15:79001600-79001800	Enhancers	Left Ventricle	heart
30	chr15:79001600-79001800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr15:79001600-79001800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
32	chr15:79001600-79001800	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr15:79001600-79001800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr15:79001600-79001800	Flanking Active TSS	Hela-S3	cervix
35	chr15:79001600-79001800	Flanking Active TSS	HSMM	muscle
36	chr15:79001600-79001800	Bivalent Enhancer	NH-A	brain
37	chr15:79001600-79001800	Flanking Active TSS	NHEK	skin
38	chr15:79001600-79002000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
39	chr15:79001600-79002000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr15:79001600-79002000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:79001600-79002000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:79001600-79002000	Flanking Active TSS	Liver	Liver
43	chr15:79001600-79002000	Enhancers	Ovary	ovary
44	chr15:79001600-79002000	Active TSS	Stomach Smooth Muscle	stomach
45	chr15:79001600-79002000	Active TSS	A549	lung
46	chr15:79001600-79002000	Enhancers	HMEC	breast
47	chr15:79001600-79002200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr15:79001600-79002200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:79001600-79002200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:79001600-79002200	Bivalent Enhancer	Primary B cells from peripheral blood	blood

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