Variant report

Variant	rs28384386
Chromosome Location	chr14:104388150-104388151
allele	C/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	ELK1	chr14:104387661-104388287	GM12878	blood:	n/a	n/a
2	ELF1	chr14:104387523-104388272	SK-N-SH	brain:	n/a	chr14:104387752-104387764
3	CHD2	chr14:104387538-104388155	Hela-S3	cervix:	n/a	chr14:104388001-104388011
4	JUND	chr14:104387640-104388157	A549	lung:	n/a	n/a
5	POLR2A	chr14:104387486-104388182	H1-hESC	embryonic stem cell:	n/a	n/a
6	BCLAF1	chr14:104387592-104388197	GM12878	blood:	n/a	chr14:104387969-104387982 chr14:104387962-104387970
7	CTCF	chr14:104387235-104388538	A549	lung:	n/a	n/a
8	MAX	chr14:104387415-104388288	A549	lung:	n/a	n/a
9	CUX1	chr14:104387507-104388229	K562	blood:	n/a	n/a
10	MAX	chr14:104387127-104388309	MCF-7	breast:	n/a	n/a
11	CTCF	chr14:104387720-104388196	K562	blood:	n/a	n/a
12	YY1	chr14:104387669-104388180	ECC-1	luminal epithelium:	n/a	chr14:104387939-104387950 chr14:104387701-104387710 chr14:104387967-104387981 chr14:104387970-104387981 chr14:104387756-104387765
13	POLR2A	chr14:104387497-104388215	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr14:104387251-104388298	K562	blood:	n/a	n/a
15	FOXP2	chr14:104387672-104388211	SK-N-MC	brain:	n/a	n/a
16	MXI1	chr14:104387919-104388191	K562	blood:	n/a	n/a
17	POLR2A	chr14:104387417-104388181	K562	blood:	n/a	n/a
18	SP4	chr14:104387701-104388231	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr14:104387541-104388153	Hela-S3	cervix:	n/a	chr14:104387698-104387708
20	RCOR1	chr14:104387492-104388157	GM12878	blood:	n/a	n/a
21	CREB1	chr14:104387651-104388232	K562	blood:	n/a	n/a
22	RFX5	chr14:104387533-104388172	HepG2	liver:	n/a	n/a
23	CREB1	chr14:104387549-104388247	GM12878	blood:	n/a	n/a
24	MAX	chr14:104387673-104388213	SK-N-SH	brain:	n/a	n/a
25	ZNF384	chr14:104387769-104388204	K562	blood:	n/a	n/a
26	CTCF	chr14:104387770-104388158	A549	lung:	n/a	n/a
27	MAX	chr14:104387660-104388229	H1-hESC	embryonic stem cell:	n/a	n/a
28	TCF12	chr14:104387567-104388241	ECC-1	luminal epithelium:	n/a	n/a
29	ZNF143	chr14:104387645-104388162	K562	blood:	n/a	chr14:104387698-104387708
30	MYC	chr14:104387343-104388166	MCF-7	breast:	n/a	n/a
31	USF1	chr14:104387717-104388164	A549	lung:	n/a	n/a
32	POLR2A	chr14:104387340-104388219	H1-hESC	embryonic stem cell:	n/a	n/a
33	ZNF143	chr14:104387596-104388177	H1-hESC	embryonic stem cell:	n/a	chr14:104387698-104387708
34	MTA3	chr14:104387178-104388193	GM12878	blood:	n/a	n/a
35	MXI1	chr14:104387326-104388179	GM12878	blood:	n/a	n/a
36	CTCF	chr14:104387742-104388183	IMR90	lung:	n/a	n/a
37	POLR2A	chr14:104387444-104388209	H1-neurons	neurons:	n/a	n/a
38	CREB1	chr14:104387737-104388229	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr14:104387452-104388172	H1-neurons	neurons:	n/a	n/a
40	TEAD4	chr14:104387664-104388244	K562	blood:	n/a	n/a
41	MXI1	chr14:104387090-104388629	SK-N-SH	brain:	n/a	n/a
42	MAX	chr14:104387344-104388257	SK-N-SH	brain:	n/a	n/a
43	MAX	chr14:104387510-104388229	GM12878	blood:	n/a	n/a
44	GTF2F1	chr14:104387419-104388224	Hela-S3	cervix:	n/a	n/a
45	HA-E2F1	chr14:104387261-104388256	MCF-7	breast:	n/a	chr14:104387750-104387762 chr14:104387874-104387883
46	PBX3	chr14:104387667-104388154	A549	lung:	n/a	n/a
47	GATA3	chr14:104387504-104388282	A549	lung:	n/a	n/a
48	POLR2A	chr14:104387227-104388255	Raji	blood:	n/a	n/a
49	TAF1	chr14:104387453-104388203	ECC-1	luminal epithelium:	n/a	n/a
50	GABPA	chr14:104387611-104388205	A549	lung:	n/a	chr14:104387873-104387887 chr14:104387873-104387884 chr14:104387873-104387882 chr14:104387870-104387884

No.	Distal block	Cell Line	Cell type
1	chr14:104380212..104384984-chr14:104386073..104389493,7	MCF-7	breast:
2	chr14:104382782..104384998-chr14:104387935..104389559,2	K562	blood:
3	chr14:104387945..104390196-chr14:104396396..104397958,2	MCF-7	breast:
4	chr14:104385710..104388983-chr14:104393675..104397966,4	MCF-7	breast:
5	chr14:104387889..104389624-chr14:104583359..104585962,2	MCF-7	breast:

Variant related genes	Relation type
C14orf2	TF binding region
ENSG00000207568	Chromatin interaction
ENSG00000156414	Chromatin interaction
ENSG00000156411	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1053419	0.88[ASN][1000 genomes]
rs11850704	0.88[ASN][1000 genomes]
rs12434277	1.00[EUR][1000 genomes]
rs17095276	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17095279	0.82[AMR][1000 genomes]
rs17101928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17101930	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17101937	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17101941	0.87[AMR][1000 genomes]
rs17101944	0.87[AMR][1000 genomes]
rs17101950	0.82[AMR][1000 genomes]
rs17101951	0.82[AMR][1000 genomes]
rs17101952	0.82[AMR][1000 genomes]
rs17101953	0.82[AMR][1000 genomes]
rs17101955	0.82[AMR][1000 genomes]
rs17101959	0.82[AMR][1000 genomes]
rs2273609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295661	0.82[AMR][1000 genomes]
rs28576742	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783311	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45523439	0.82[AMR][1000 genomes]
rs7140812	0.96[EUR][1000 genomes]
rs74086744	0.88[ASN][1000 genomes]
rs74086746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74086758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8014519	0.96[EUR][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	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv902318	chr14:104255083-104464809	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
7	nsv1048353	chr14:104361402-104483286	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv902322	chr14:104365310-104464809	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv902323	chr14:104381687-104464809	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28384386	C14orf2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104386200-104388400	Active TSS	Hela-S3	cervix
2	chr14:104386600-104388200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr14:104386800-104388200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr14:104386800-104388200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:104386800-104388200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr14:104386800-104388200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr14:104386800-104388200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr14:104386800-104388200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr14:104386800-104388200	Active TSS	Brain Angular Gyrus	brain
10	chr14:104386800-104388200	Active TSS	Right Atrium	heart
11	chr14:104386800-104388200	Active TSS	GM12878-XiMat	blood
12	chr14:104386800-104388200	Active TSS	K562	blood
13	chr14:104386800-104388400	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr14:104386800-104388400	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr14:104386800-104388400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr14:104386800-104388400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr14:104386800-104388400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr14:104386800-104388400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr14:104386800-104388400	Active TSS	A549	lung
20	chr14:104386800-104388400	Active TSS	HSMM	muscle
21	chr14:104386800-104388400	Active TSS	NHLF	lung
22	chr14:104387000-104388200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr14:104387000-104388200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr14:104387000-104388200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr14:104387000-104388200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr14:104387000-104388200	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr14:104387000-104388200	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr14:104387000-104388200	Active TSS	Placenta	Placenta
29	chr14:104387000-104388200	Active TSS	Rectal Smooth Muscle	rectum
30	chr14:104387000-104388200	Active TSS	NH-A	brain
31	chr14:104387000-104388200	Active TSS	NHDF-Ad	bronchial
32	chr14:104387000-104388400	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr14:104387000-104388400	Active TSS	Brain Cingulate Gyrus	brain
34	chr14:104387200-104388200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr14:104387200-104388400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr14:104387200-104388400	Active TSS	Brain Hippocampus Middle	brain
37	chr14:104387200-104388400	Active TSS	Right Ventricle	heart
38	chr14:104387200-104388400	Active TSS	NHEK	skin
39	chr14:104387400-104388200	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr14:104387400-104388200	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr14:104387400-104388200	Active TSS	Brain Substantia Nigra	brain
42	chr14:104387400-104388200	Active TSS	Fetal Heart	heart
43	chr14:104387400-104388200	Active TSS	Fetal Lung	lung
44	chr14:104387400-104388200	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr14:104387400-104388200	Active TSS	HSMMtube	muscle
46	chr14:104387400-104388200	Active TSS	Osteobl	bone
47	chr14:104387400-104388400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr14:104387400-104388400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr14:104387400-104388400	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr14:104387400-104388400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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