Variant report

Variant	rs12885295
Chromosome Location	chr14:21553545-21553546
allele	A/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	POLR2A	chr14:21553296-21553716	MCF10A-Er-Src	breast:	n/a	n/a
2	HNF4A	chr14:21553351-21553659	HepG2	liver:	n/a	chr14:21553534-21553549 chr14:21553535-21553549 chr14:21553534-21553549 chr14:21553536-21553548 chr14:21553534-21553549 chr14:21553534-21553549 chr14:21553534-21553549
3	STAT3	chr14:21553495-21553755	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr14:21553296-21554084	HepG2	liver:	n/a	n/a
5	HNF4G	chr14:21553343-21553722	HepG2	liver:	n/a	chr14:21553535-21553550 chr14:21553534-21553549 chr14:21553535-21553549 chr14:21553534-21553549 chr14:21553536-21553548 chr14:21553534-21553549 chr14:21553534-21553549
6	GATA3	chr14:21553105-21553681	SK-N-SH	brain:	n/a	chr14:21553466-21553482 chr14:21553278-21553294 chr14:21553282-21553291
7	GABPA	chr14:21553434-21553857	HL-60	blood:	n/a	n/a
8	SPI1	chr14:21553444-21553805	HL-60	blood:	n/a	n/a
9	SPI1	chr14:21553343-21553930	HL-60	blood:	n/a	n/a
10	GATA3	chr14:21553177-21553758	SK-N-SH	brain:	n/a	chr14:21553466-21553482 chr14:21553278-21553294 chr14:21553282-21553291
11	POLR2A	chr14:21552867-21553547	SK-N-SH	brain:	n/a	n/a
12	HNF4A	chr14:21553315-21553660	HepG2	liver:	n/a	chr14:21553534-21553549 chr14:21553535-21553549 chr14:21553534-21553549 chr14:21553536-21553548 chr14:21553534-21553549 chr14:21553534-21553549 chr14:21553534-21553549
13	CEBPB	chr14:21553472-21553879	IMR90	lung:	n/a	n/a
14	ARID3A	chr14:21553374-21553644	HepG2	liver:	n/a	n/a
15	POLR2A	chr14:21551966-21554246	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr14:21553343-21553929	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr14:21553164-21553554	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:21550533..21554040-chr14:21555474..21559847,4	K562	blood:
2	chr14:21550786..21552632-chr14:21553088..21555005,3	MCF-7	breast:
3	chr14:21551229..21553678-chr14:21572331..21574679,2	K562	blood:
4	chr14:21551066..21553678-chr14:21572331..21574679,3	K562	blood:
5	chr14:21543597..21548802-chr14:21549999..21554096,6	MCF-7	breast:
6	chr14:21547728..21550194-chr14:21553022..21555412,3	K562	blood:
7	chr14:21536527..21539599-chr14:21551336..21554432,4	MCF-7	breast:

Variant related genes	Relation type
ARHGEF40	TF binding region
ENSG00000165804	Chromatin interaction
ENSG00000165801	Chromatin interaction
ENSG00000165795	Chromatin interaction
ENSG00000258714	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1243473	0.89[CEU][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12885183	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12889267	0.84[ASN][1000 genomes]
rs12891708	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1952512	1.00[JPT][hapmap]
rs2319627	1.00[JPT][hapmap]
rs3827910	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
2	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv916319	chr14:21507092-21896590	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv826882	chr14:21511021-21604201	Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv530770	chr14:21526410-21852363	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
8	nsv528337	chr14:21540863-21565189	Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv525724	chr14:21540863-21574690	Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21540800-21554000	Weak transcription	Primary B cells from cord blood	blood
2	chr14:21540800-21554800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:21541000-21554000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:21541000-21554400	Strong transcription	Lung	lung
5	chr14:21541000-21555000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr14:21541000-21555200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr14:21541000-21555200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr14:21541000-21555600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr14:21541000-21561000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr14:21541200-21553600	Weak transcription	Small Intestine	intestine
11	chr14:21541200-21554600	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr14:21541200-21555000	Strong transcription	Aorta	Aorta
13	chr14:21541200-21555200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr14:21541200-21557000	Weak transcription	Hela-S3	cervix
15	chr14:21541200-21561400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:21541400-21554400	Strong transcription	NHLF	lung
17	chr14:21541400-21554800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr14:21541400-21554800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:21541400-21555000	Strong transcription	Brain Germinal Matrix	brain
20	chr14:21541400-21555200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr14:21541400-21555200	Strong transcription	Brain Cingulate Gyrus	brain
22	chr14:21541400-21555200	Strong transcription	Colonic Mucosa	Colon
23	chr14:21541400-21555600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr14:21541400-21558000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr14:21541400-21560200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr14:21541400-21560200	Strong transcription	Placenta	Placenta
27	chr14:21541600-21553800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr14:21541600-21555000	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr14:21541600-21555200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:21541600-21555200	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr14:21541600-21555400	Strong transcription	Brain Hippocampus Middle	brain
32	chr14:21541600-21555800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr14:21541600-21557000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr14:21541600-21558800	Strong transcription	Fetal Lung	lung
35	chr14:21541600-21560400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr14:21541800-21555600	Strong transcription	Ovary	ovary
37	chr14:21542000-21555200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr14:21542000-21559800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr14:21542200-21554000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr14:21542400-21554800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr14:21542400-21555200	Strong transcription	Fetal Stomach	stomach
42	chr14:21542400-21560200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr14:21542400-21560400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr14:21542600-21554800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr14:21542800-21553800	Strong transcription	Brain Anterior Caudate	brain
46	chr14:21543200-21554600	Strong transcription	Fetal Brain Female	brain
47	chr14:21543200-21555200	Strong transcription	Fetal Muscle Leg	muscle
48	chr14:21543400-21555000	Strong transcription	Brain Substantia Nigra	brain
49	chr14:21543400-21555200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr14:21543800-21561400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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