Variant report

Variant	rs12446288
Chromosome Location	chr16:30388709-30388710
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	HCFC1	chr16:30388524-30390500	Hela-S3	cervix:	n/a	n/a
2	CREB1	chr16:30388640-30390742	HepG2	liver:	n/a	n/a
3	MAX	chr16:30388641-30390577	ECC-1	luminal epithelium:	n/a	n/a
4	HEY1	chr16:30388687-30390118	K562	blood:	n/a	chr16:30389037-30389052
5	POLR2A	chr16:30388059-30391180	HepG2	liver:	n/a	n/a
6	EGR1	chr16:30388707-30390310	HCT-116	colon:	n/a	chr16:30388782-30388789 chr16:30389558-30389572
7	TRIM28	chr16:30388650-30390007	K562	blood:	n/a	n/a
8	POLR2A	chr16:30388692-30390462	PANC-1	pancreas:	n/a	n/a
9	EGR1	chr16:30388678-30389877	K562	blood:	n/a	chr16:30388782-30388789 chr16:30389558-30389572
10	POLR2A	chr16:30388507-30390948	GM12878	blood:	n/a	n/a
11	MAX	chr16:30388562-30390688	HCT-116	colon:	n/a	n/a
12	POLR2A	chr16:30388356-30391169	K562	blood:	n/a	n/a
13	POLR2A	chr16:30388635-30390948	GM12892	blood:	n/a	n/a
14	MTA3	chr16:30388533-30390824	GM12878	blood:	n/a	n/a
15	STAT5A	chr16:30388637-30390220	GM12878	blood:	n/a	n/a
16	POLR2A	chr16:30388581-30390913	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr16:30388572-30390647	H1-hESC	embryonic stem cell:	n/a	n/a
18	NR2F2	chr16:30388528-30390332	K562	blood:	n/a	n/a
19	MXI1	chr16:30388530-30391046	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr16:30388604-30390158	GM12878	blood:	n/a	n/a
21	TCF12	chr16:30388610-30390184	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr16:30388556-30390078	HL-60	blood:	n/a	n/a
23	TEAD4	chr16:30388506-30388968	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr16:30388431-30390190	HL-60	blood:	n/a	n/a
25	POLR2A	chr16:30388628-30390172	GM12892	blood:	n/a	n/a
26	ELF1	chr16:30388689-30390102	MCF-7	breast:	n/a	chr16:30389062-30389074
27	POLR2A	chr16:30388650-30390591	ECC-1	luminal epithelium:	n/a	n/a
28	REST	chr16:30388618-30390953	H1-neurons	neurons:	n/a	n/a
29	GTF2F1	chr16:30388644-30388810	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr16:30388637-30390049	MCF10A-Er-Src	breast:	n/a	n/a
31	ELF1	chr16:30388688-30390203	K562	blood:	n/a	chr16:30389062-30389074
32	MXI1	chr16:30388622-30390795	IMR90	lung:	n/a	n/a
33	POLR2A	chr16:30388611-30390084	K562	blood:	n/a	n/a
34	MAX	chr16:30388649-30390513	K562	blood:	n/a	n/a
35	POLR2A	chr16:30388409-30390931	K562	blood:	n/a	n/a
36	MAZ	chr16:30388680-30390702	IMR90	lung:	n/a	n/a
37	HEY1	chr16:30388538-30390561	K562	blood:	n/a	chr16:30390507-30390522 chr16:30389037-30389052
38	POLR2A	chr16:30388644-30390113	GM12892	blood:	n/a	n/a
39	POLR2A	chr16:30388599-30390603	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr16:30388547-30390673	MCF-7	breast:	n/a	n/a
41	PAX5	chr16:30388648-30389312	GM12878	blood:	n/a	chr16:30389029-30389048
42	MAX	chr16:30388618-30390680	A549	lung:	n/a	n/a
43	EGR1	chr16:30388629-30390126	K562	blood:	n/a	chr16:30388782-30388789 chr16:30389558-30389572
44	CREB1	chr16:30388648-30390471	A549	lung:	n/a	n/a
45	SIN3AK20	chr16:30388642-30390726	MCF-7	breast:	n/a	n/a
46	POLR2A	chr16:30388616-30390592	K562	blood:	n/a	n/a
47	SP1	chr16:30388663-30390638	H1-hESC	embryonic stem cell:	n/a	chr16:30389037-30389046 chr16:30389054-30389068 chr16:30389035-30389047 chr16:30389035-30389047 chr16:30390511-30390523 chr16:30389056-30389063 chr16:30390511-30390523 chr16:30389036-30389045 chr16:30389037-30389046 chr16:30390276-30390285 chr16:30390116-30390128 chr16:30390081-30390095
48	PML	chr16:30388573-30390691	GM12878	blood:	n/a	n/a
49	POLR2A	chr16:30388654-30390245	PFSK-1	brain:	n/a	n/a
50	TCF12	chr16:30388524-30390457	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30385968..30392864-chr16:30403786..30414800,30	MCF-7	breast:
2	chr16:30388636..30390782-chr16:30456126..30458757,2	K562	blood:
3	chr16:30387323..30391526-chr16:30418280..30422943,8	MCF-7	breast:
4	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
5	chr16:30104324..30107444-chr16:30387939..30391317,4	K562	blood:
6	chr16:30365100..30369727-chr16:30387622..30391726,6	MCF-7	breast:
7	chr16:30387676..30396507-chr16:30404234..30411930,28	K562	blood:
8	chr16:30387917..30393231-chr16:30417396..30420787,10	MCF-7	breast:
9	chr16:30364152..30368341-chr16:30388051..30392327,13	K562	blood:
10	chr16:30386516..30389476-chr16:30440230..30442571,3	K562	blood:
11	chr16:30388636..30392264-chr16:30455799..30458757,3	K562	blood:
12	chr16:30364024..30368341-chr16:30387690..30394486,12	K562	blood:
13	chr15:41624298..41625139-chr16:30388538..30389381,2	NB4	blood:
14	chr16:30128056..30129956-chr16:30388076..30390685,2	K562	blood:
15	chr16:30384243..30394929-chr16:30405602..30409736,14	K562	blood:
16	chr16:30378594..30387256-chr16:30387352..30391288,21	MCF-7	breast:

Variant related genes	Relation type
MYLPF	TF binding region
ZNF48	TF binding region
ENSG00000260219	Chromatin interaction
ENSG00000104147	Chromatin interaction
ENSG00000179965	Chromatin interaction
ENSG00000102882	Chromatin interaction
ENSG00000090238	Chromatin interaction
ENSG00000169221	Chromatin interaction
ENSG00000180209	Chromatin interaction
ENSG00000137804	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000179958	Chromatin interaction
ENSG00000179918	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000169217	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11150586	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs11642676	0.91[EUR][1000 genomes]
rs11645581	0.86[EUR][1000 genomes]
rs11646130	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs11862806	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11863150	0.82[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12447833	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12921440	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12930787	0.84[EUR][1000 genomes]
rs13333093	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35480350	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs35598865	1.00[JPT][hapmap]
rs3574	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4465620	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4787642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4787643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4788414	0.81[EUR][1000 genomes]
rs62055459	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6565178	0.81[EUR][1000 genomes]
rs6565180	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6565182	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs6565183	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68051857	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7203359	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73532600	0.90[EUR][1000 genomes]
rs8046445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8049108	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8050812	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8051096	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs8060853	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9888967	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9921711	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12446288	SEPHS2	cis	cerebellum	SCAN
rs12446288	RP11-231C14.4	cis	Artery Tibial	GTEx
rs12446288	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs12446288	GDPD3	cis	cerebellum	SCAN
rs12446288	TBX6	cis	parietal	SCAN
rs12446288	MAPK3	cis	parietal	SCAN
rs12446288	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30383200-30388800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr16:30383200-30388800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:30383800-30388800	Weak transcription	Right Ventricle	heart
4	chr16:30385800-30388800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr16:30386200-30390800	Active TSS	HSMMtube	muscle
6	chr16:30386800-30388800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:30386800-30388800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr16:30386800-30388800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr16:30386800-30388800	Enhancers	Placenta	Placenta
10	chr16:30386800-30390000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
11	chr16:30387000-30388800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
12	chr16:30387200-30388800	Enhancers	Psoas Muscle	Psoas
13	chr16:30387400-30388800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr16:30387800-30388800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:30387800-30388800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr16:30388000-30388800	Enhancers	Primary B cells from cord blood	blood
17	chr16:30388200-30389400	Flanking Active TSS	HepG2	liver
18	chr16:30388400-30388800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:30388400-30388800	Enhancers	Colon Smooth Muscle	Colon
20	chr16:30388400-30388800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr16:30388400-30389000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr16:30388400-30389200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:30388400-30389200	Enhancers	Spleen	Spleen
24	chr16:30388400-30389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr16:30388400-30389600	Flanking Active TSS	Dnd41	blood
26	chr16:30388600-30388800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr16:30388600-30388800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr16:30388600-30388800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr16:30388600-30388800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
30	chr16:30388600-30388800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:30388600-30388800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr16:30388600-30388800	Flanking Active TSS	Fetal Kidney	kidney
33	chr16:30388600-30388800	Enhancers	Left Ventricle	heart
34	chr16:30388600-30388800	Enhancers	Pancreas	Pancrea
35	chr16:30388600-30388800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr16:30388600-30388800	Flanking Active TSS	Thymus	Thymus
37	chr16:30388600-30388800	Enhancers	NH-A	brain
38	chr16:30388600-30389000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
39	chr16:30388600-30389000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr16:30388600-30389000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr16:30388600-30389000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr16:30388600-30389000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr16:30388600-30389000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr16:30388600-30389000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr16:30388600-30389000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr16:30388600-30389000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr16:30388600-30389000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr16:30388600-30389000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr16:30388600-30389000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr16:30388600-30389000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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