Variant report

Variant	rs28513222
Chromosome Location	chr14:104028069-104028070
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	POU2F2	chr14:104028019-104028556	GM12891	blood:	n/a	n/a
2	POLR2A	chr14:104028038-104029632	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr14:104027813-104029763	HepG2	liver:	n/a	n/a
4	POLR2A	chr14:104027723-104029500	IMR90	lung:	n/a	n/a
5	JUND	chr14:104027577-104028272	H1-hESC	embryonic stem cell:	n/a	chr14:104027796-104027807 chr14:104027897-104027906
6	MYC	chr14:104028059-104028542	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr14:104027997-104029923	HUVEC	blood vessel:	n/a	n/a
8	MAX	chr14:104027988-104029903	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr14:104028065-104029756	GM12892	blood:	n/a	n/a
10	SPI1	chr14:104027931-104028130	K562	blood:	n/a	chr14:104028025-104028038
11	POLR2A	chr14:104028049-104029813	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr14:104028059-104028407	GM12878	blood:	n/a	chr14:104028385-104028399
13	POLR2A	chr14:104027750-104028109	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr14:104027840-104028110	MCF-7	breast:	n/a	n/a
15	SIN3A	chr14:104027720-104030129	H1-hESC	embryonic stem cell:	n/a	chr14:104028758-104028771 chr14:104028792-104028805 chr14:104028844-104028855 chr14:104028533-104028544 chr14:104028851-104028864 chr14:104029113-104029126 chr14:104029095-104029108
16	SPI1	chr14:104027812-104028545	HL-60	blood:	n/a	chr14:104028025-104028038
17	POLR2A	chr14:104027673-104029763	GM12878	blood:	n/a	n/a
18	SIN3AK20	chr14:104028035-104029746	SK-N-SH	brain:	n/a	n/a
19	WRNIP1	chr14:104027830-104028558	GM12878	blood:	n/a	n/a
20	CREB1	chr14:104027540-104028133	H1-hESC	embryonic stem cell:	n/a	n/a
21	HCFC1	chr14:104027237-104030166	Hela-S3	cervix:	n/a	n/a
22	SIN3AK20	chr14:104027394-104030066	MCF-7	breast:	n/a	n/a
23	POU2F2	chr14:104027977-104028526	GM12878	blood:	n/a	n/a
24	MXI1	chr14:104028044-104030134	IMR90	lung:	n/a	n/a
25	SIN3A	chr14:104027988-104029799	GM12878	blood:	n/a	chr14:104028758-104028771 chr14:104028792-104028805 chr14:104028844-104028855 chr14:104028533-104028544 chr14:104028851-104028864 chr14:104029113-104029126 chr14:104029095-104029108
26	SMC3	chr14:104027847-104028294	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr14:104027853-104029809	Hela-S3	cervix:	n/a	n/a
28	CHD2	chr14:104027988-104028292	H1-hESC	embryonic stem cell:	n/a	n/a
29	RCOR1	chr14:104027726-104028114	Hela-S3	cervix:	n/a	n/a
30	REST	chr14:104027727-104029942	H1-neurons	neurons:	n/a	chr14:104028758-104028771 chr14:104028121-104028130 chr14:104028792-104028805 chr14:104028123-104028130 chr14:104029104-104029117 chr14:104028789-104028802 chr14:104028796-104028805
31	POLR2A	chr14:104027824-104030167	GM12891	blood:	n/a	n/a
32	SMC3	chr14:104028052-104028070	HepG2	liver:	n/a	n/a
33	HA-E2F1	chr14:104027559-104029847	MCF-7	breast:	n/a	chr14:104028207-104028221 chr14:104028209-104028217 chr14:104028209-104028217 chr14:104028673-104028688 chr14:104029236-104029245
34	POLR2A	chr14:104028065-104029730	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr14:104027695-104029796	Hela-S3	cervix:	n/a	n/a
36	EP300	chr14:104027440-104028566	ECC-1	luminal epithelium:	n/a	n/a
37	GTF2F1	chr14:104028013-104028132	H1-hESC	embryonic stem cell:	n/a	n/a
38	GABPA	chr14:104027612-104029881	MCF-7	breast:	n/a	n/a
39	MXI1	chr14:104027798-104030910	SK-N-SH	brain:	n/a	chr14:104030620-104030635 chr14:104030622-104030637
40	POLR2A	chr14:104028026-104029723	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr14:104027621-104029923	MCF10A-Er-Src	breast:	n/a	n/a
42	ZNF263	chr14:104027545-104029148	HEK293-T-REx	kidney:	n/a	chr14:104028713-104028722 chr14:104028399-104028408
43	POLR2A	chr14:104028067-104029578	GM19099	blood:	n/a	n/a
44	RUNX3	chr14:104028036-104029522	GM12878	blood:	n/a	n/a
45	MAX	chr14:104027750-104030033	Hela-S3	cervix:	n/a	n/a
46	MAX	chr14:104027574-104029883	MCF-7	breast:	n/a	n/a
47	POLR2A	chr14:104027813-104028138	H1-hESC	embryonic stem cell:	n/a	n/a
48	MYC	chr14:104027773-104028332	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr14:104028016-104029757	H1-neurons	neurons:	n/a	n/a
50	MXI1	chr14:104027879-104029711	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:104026845..104031617-chr14:104090112..104098528,12	MCF-7	breast:
2	chr14:104016689..104020988-chr14:104027518..104030448,6	MCF-7	breast:
3	chr14:103983696..103988397-chr14:104026059..104029809,6	K562	blood:
4	chr14:103992721..103998040-chr14:104027797..104030842,4	MCF-7	breast:
5	chr14:104026026..104030833-chr14:104180410..104184978,6	MCF-7	breast:
6	chr14:104014533..104016298-chr14:104025800..104028102,2	K562	blood:
7	chr14:103799415..103801924-chr14:104027086..104029565,3	MCF-7	breast:
8	chr14:104018005..104022715-chr14:104023184..104028959,7	K562	blood:
9	chr14:104026574..104032100-chr14:104033737..104038565,9	MCF-7	breast:
10	chr14:103985364..103989946-chr14:104026445..104030227,8	MCF-7	breast:
11	chr14:104003474..104006501-chr14:104024765..104028078,3	MCF-7	breast:
12	chr14:104027061..104029959-chr14:104033088..104037337,3	K562	blood:
13	chr14:104027610..104029440-chr14:104145265..104147418,2	MCF-7	breast:
14	chr14:104027886..104033252-chr14:104178637..104183670,7	MCF-7	breast:
15	chr14:104027275..104029645-chr9:131939860..131941591,2	MCF-7	breast:
16	chr14:103992298..103994293-chr14:104026567..104028145,2	K562	blood:
17	chr14:104026767..104030601-chr14:104092111..104097061,5	MCF-7	breast:

Variant related genes	Relation type
APOPT1	TF binding region
ENSG00000256500	TF binding region
KLC1	TF binding region
ENSG00000256053	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000188483	Chromatin interaction
ENSG00000100664	Chromatin interaction
ENSG00000126215	Chromatin interaction
ENSG00000201184	Chromatin interaction
ENSG00000269963	Chromatin interaction
ENSG00000166166	Chromatin interaction
ENSG00000260285	Chromatin interaction
ENSG00000166165	Chromatin interaction
ENSG00000258851	Chromatin interaction
ENSG00000126214	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10140410	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10143293	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10149249	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11621777	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11626658	0.89[EUR][1000 genomes]
rs2274268	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274269	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28514618	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28660416	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28744517	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55864158	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56017123	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57447494	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59281218	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60802358	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61996716	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61996717	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61996718	0.86[ASN][1000 genomes]
rs61996721	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7142883	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7154587	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154948	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942863	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902297	chr14:103956182-104061646	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902298	chr14:103959289-104061646	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv902299	chr14:103967504-104061646	Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv902303	chr14:103979953-104034746	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv902304	chr14:103979953-104061646	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv902305	chr14:103979953-104073551	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
10	esv1839595	chr14:103987140-104034746	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv976818	chr14:104023424-104029394	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28513222	APOPT1	cis	Muscle Skeletal	GTEx
rs28513222	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs28513222	BAG5	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104027000-104028400	Flanking Active TSS	Brain Germinal Matrix	brain
2	chr14:104027000-104028400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr14:104027000-104028400	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr14:104027000-104028600	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr14:104027200-104028200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr14:104027200-104028200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr14:104027200-104028200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr14:104027200-104028200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr14:104027200-104028200	Flanking Active TSS	HUVEC	blood vessel
10	chr14:104027200-104028400	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr14:104027200-104028400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr14:104027200-104028400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:104027200-104028400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr14:104027200-104028400	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr14:104027200-104028400	Flanking Active TSS	Fetal Brain Female	brain
16	chr14:104027200-104028400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr14:104027200-104028400	Flanking Active TSS	Dnd41	blood
18	chr14:104027200-104028600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr14:104027200-104028600	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr14:104027400-104028200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:104027400-104028200	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr14:104027400-104028200	Flanking Active TSS	Fetal Heart	heart
23	chr14:104027400-104028200	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr14:104027400-104028200	Flanking Active TSS	K562	blood
25	chr14:104027400-104028200	Flanking Active TSS	NH-A	brain
26	chr14:104027400-104028400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr14:104027400-104028400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr14:104027400-104028400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr14:104027400-104028400	Flanking Active TSS	Osteobl	bone
30	chr14:104027400-104028600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr14:104027400-104030600	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr14:104027400-104030800	Active TSS	H1 Cell Line	embryonic stem cell
33	chr14:104027400-104030800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr14:104027600-104028200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr14:104027600-104028200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr14:104027600-104028200	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr14:104027600-104028200	Flanking Active TSS	Fetal Stomach	stomach
38	chr14:104027600-104028200	Flanking Active TSS	Fetal Thymus	thymus
39	chr14:104027600-104028200	Flanking Active TSS	Left Ventricle	heart
40	chr14:104027600-104028200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr14:104027600-104028200	Flanking Active TSS	Thymus	Thymus
42	chr14:104027600-104028400	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr14:104027600-104028400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr14:104027600-104028400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr14:104027600-104028400	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr14:104027600-104028400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr14:104027600-104028400	Flanking Active TSS	Fetal Muscle Trunk	muscle
48	chr14:104027600-104028400	Flanking Active TSS	Placenta	Placenta
49	chr14:104027600-104028400	Flanking Active TSS	Pancreas	Pancrea
50	chr14:104027600-104028400	Flanking Active TSS	Placenta Amnion	Placenta Amnion

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