Variant report

Variant	rs12050290
Chromosome Location	chr14:35008043-35008044
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr14:35007600-35009289	SK-N-SH	brain:	n/a	n/a
2	WRNIP1	chr14:35007996-35008190	GM12878	blood:	n/a	n/a
3	ZC3H11A	chr14:35007948-35008140	K562	blood:	n/a	n/a
4	NFIC	chr14:35008016-35009170	HepG2	liver:	n/a	n/a
5	MYC	chr14:35007786-35009082	MCF10A-Er-Src	breast:	n/a	chr14:35008525-35008532
6	CHD1	chr14:35007665-35009150	IMR90	lung:	n/a	chr14:35008580-35008590
7	POLR2A	chr14:35007986-35009835	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA2	chr14:35007889-35009540	HepG2	liver:	n/a	n/a
9	POLR2A	chr14:35007954-35008077	HepG2	liver:	n/a	n/a
10	POLR2A	chr14:35007979-35009139	Hela-S3	cervix:	n/a	n/a
11	MBD4	chr14:35008000-35009163	HepG2	liver:	n/a	n/a
12	HCFC1	chr14:35007928-35009595	Hela-S3	cervix:	n/a	n/a
13	REST	chr14:35008024-35009236	H1-neurons	neurons:	n/a	n/a
14	CHD1	chr14:35007894-35008967	GM12878	blood:	n/a	chr14:35008580-35008590
15	MAX	chr14:35007738-35009163	HepG2	liver:	n/a	chr14:35008525-35008532
16	POLR2A	chr14:35007694-35009897	MCF10A-Er-Src	breast:	n/a	n/a
17	MAFK	chr14:35007926-35008103	HepG2	liver:	n/a	n/a
18	MBD4	chr14:35007830-35009108	HepG2	liver:	n/a	n/a
19	MYBL2	chr14:35007950-35011284	HepG2	liver:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:35007630..35008465-chr16:73238858..73239382,2	MCF-7	breast:
2	chr14:35004626..35011116-chr14:35015634..35020787,10	MCF-7	breast:
3	chr14:35005506..35011243-chr14:35020994..35025666,12	MCF-7	breast:
4	chr14:35005284..35011388-chr14:35017198..35025900,23	MCF-7	breast:
5	chr14:35008040..35009005-chr16:27214684..27215320,2	Hela-S3	cervix:
6	chr14:35005764..35008884-chr14:35021719..35025749,6	K562	blood:
7	chr14:34992410..34994552-chr14:35006648..35008744,2	MCF-7	breast:
8	chr14:35007550..35010317-chr14:35342022..35344512,2	K562	blood:
9	chr14:35007550..35010391-chr14:35343012..35345148,2	K562	blood:
10	chr14:34792427..34794155-chr14:35007082..35008607,2	MCF-7	breast:
11	chr14:35003178..35006952-chr14:35007318..35009026,4	MCF-7	breast:
12	chr14:34929666..34933656-chr14:35005721..35010391,9	K562	blood:
13	chr14:34929915..34933661-chr14:35006959..35010400,6	MCF-7	breast:
14	chr14:35005104..35007114-chr14:35007414..35009874,3	K562	blood:
15	chr14:34930470..34932730-chr14:35007965..35010227,2	K562	blood:
16	chr14:34990714..34993643-chr14:35006292..35008810,2	K562	blood:

No data

Variant related genes	Relation type
EAPP	TF binding region
ENSG00000206596	Chromatin interaction
ENSG00000165389	Chromatin interaction
ENSG00000198604	Chromatin interaction
ENSG00000155666	Chromatin interaction
ENSG00000206588	Chromatin interaction
ENSG00000129518	Chromatin interaction
ENSG00000129521	Chromatin interaction
ENSG00000258738	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12434523	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12435717	0.91[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs12588228	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12588878	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12589576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12590563	0.80[AFR][1000 genomes]
rs12878227	0.82[EUR][1000 genomes]
rs12878854	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12882703	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12884997	0.81[EUR][1000 genomes]
rs12885352	0.81[EUR][1000 genomes]
rs12894795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12895007	0.80[AFR][1000 genomes]
rs12895640	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs13826	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs17524152	0.91[ASW][hapmap];0.95[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs28515732	0.82[EUR][1000 genomes]
rs34068551	0.81[EUR][1000 genomes]
rs34356189	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34437689	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34479175	0.81[EUR][1000 genomes]
rs35091031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35194168	0.82[EUR][1000 genomes]
rs35415402	0.80[EUR][1000 genomes]
rs35804665	0.83[AFR][1000 genomes]
rs4368076	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4592561	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4628872	0.81[EUR][1000 genomes]
rs55858014	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56801633	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61316540	0.81[EUR][1000 genomes]
rs61979674	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61979715	0.81[EUR][1000 genomes]
rs61981527	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61981529	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6650487	0.95[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap]
rs7146042	0.95[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap]
rs7158829	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040980	chr14:34345018-35255592	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv901600	chr14:34895977-35010041	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1048408	chr14:34958352-35255592	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1049048	chr14:34969406-35048672	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1042294	chr14:34974774-35017859	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1053274	chr14:34980184-35020973	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1037503	chr14:34980184-35027115	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
8	nsv564194	chr14:34985645-35029396	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
9	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12050290	AKAP6	cis	parietal	SCAN
rs12050290	FAM177A1	cis	cerebellum	SCAN
rs12050290	EAPP	cis	cerebellum	SCAN
rs12050290	EAPP	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:34986600-35008400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:34988000-35008400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:34992200-35008200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:35002200-35008400	Weak transcription	Lung	lung
5	chr14:35006400-35008400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr14:35007000-35008400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:35007000-35008400	Weak transcription	Gastric	stomach
8	chr14:35007000-35009400	Active TSS	Fetal Intestine Large	intestine
9	chr14:35007000-35009400	Active TSS	GM12878-XiMat	blood
10	chr14:35007000-35009600	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr14:35007000-35009800	Active TSS	Colonic Mucosa	Colon
12	chr14:35007200-35008200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:35007200-35008600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr14:35007200-35008800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:35007200-35009400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr14:35007200-35009400	Active TSS	Fetal Intestine Small	intestine
17	chr14:35007200-35009400	Active TSS	Ovary	ovary
18	chr14:35007200-35009400	Active TSS	Right Atrium	heart
19	chr14:35007200-35009400	Active TSS	Right Ventricle	heart
20	chr14:35007200-35009400	Active TSS	K562	blood
21	chr14:35007200-35009400	Active TSS	NHLF	lung
22	chr14:35007200-35009800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr14:35007400-35008800	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr14:35007400-35009400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:35007400-35009400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr14:35007400-35009800	Active TSS	Hela-S3	cervix
27	chr14:35007600-35008200	Flanking Active TSS	Liver	Liver
28	chr14:35007600-35008200	Flanking Active TSS	Fetal Lung	lung
29	chr14:35007600-35008200	Flanking Active TSS	Fetal Thymus	thymus
30	chr14:35007600-35008200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr14:35007600-35008200	Flanking Active TSS	Dnd41	blood
32	chr14:35007600-35008200	Flanking Active TSS	HMEC	breast
33	chr14:35007600-35008200	Flanking Active TSS	HUVEC	blood vessel
34	chr14:35007600-35008200	Flanking Active TSS	NH-A	brain
35	chr14:35007600-35008400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr14:35007600-35008400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr14:35007600-35008400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr14:35007600-35008400	Flanking Active TSS	Osteobl	bone
39	chr14:35007600-35009400	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr14:35007600-35009400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr14:35007600-35009400	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr14:35007600-35009400	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr14:35007600-35009400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr14:35007600-35009400	Active TSS	Aorta	Aorta
45	chr14:35007600-35009400	Active TSS	Psoas Muscle	Psoas
46	chr14:35007600-35009400	Active TSS	Rectal Smooth Muscle	rectum
47	chr14:35007600-35009400	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr14:35007600-35009400	Active TSS	A549	lung
49	chr14:35007600-35009400	Active TSS	NHDF-Ad	bronchial
50	chr14:35007600-35009800	Active TSS	HUES64 Cell Line	embryonic stem cell

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