Variant report

Variant	rs12891613
Chromosome Location	chr14:24903964-24903965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:24903461-24912546	GM12892	blood:	n/a	n/a
2	POLR2A	chr14:24903879-24904007	K562	blood:	n/a	n/a
3	POLR2A	chr14:24903728-24905618	GM12892	blood:	n/a	n/a
4	POLR2A	chr14:24903889-24904166	HCT-116	colon:	n/a	n/a
5	POLR2A	chr14:24903683-24913003	HepG2	liver:	n/a	n/a
6	POLR2A	chr14:24903901-24904243	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr14:24903885-24905007	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr14:24903880-24912404	K562	blood:	n/a	n/a
9	POLR2A	chr14:24903891-24904479	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr14:24903227-24904365	GM12878	blood:	n/a	n/a
11	POLR2A	chr14:24903590-24904048	HepG2	liver:	n/a	n/a
12	POLR2A	chr14:24903864-24904207	GM12891	blood:	n/a	n/a
13	POLR2A	chr14:24903904-24904823	IMR90	lung:	n/a	n/a
14	HEY1	chr14:24903881-24904905	HepG2	liver:	n/a	n/a
15	POLR2A	chr14:24903864-24904197	K562	blood:	n/a	n/a
16	POLR2A	chr14:24903772-24904641	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr14:24903950-24904308	HCT-116	colon:	n/a	n/a
18	POLR2A	chr14:24903927-24904439	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr14:24903172-24905101	PBDE	blood:	n/a	n/a
20	POLR2A	chr14:24903800-24905057	HepG2	liver:	n/a	n/a
21	POLR2A	chr14:24903850-24904231	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr14:24903877-24904284	U87	brain:	n/a	n/a
23	POLR2A	chr14:24903587-24905239	GM12892	blood:	n/a	n/a
24	POLR2A	chr14:24903850-24904154	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr14:24903804-24905128	GM12891	blood:	n/a	n/a
26	POLR2A	chr14:24903929-24904885	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr14:24903373-24912013	A549	lung:	n/a	n/a
28	POLR2A	chr14:24903826-24905082	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr14:24903817-24905139	GM12892	blood:	n/a	n/a
30	POLR2A	chr14:24902929-24912574	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:24778484..24781723-chr14:24903121..24905574,3	MCF-7	breast:
2	chr14:24784156..24786411-chr14:24902043..24903972,2	MCF-7	breast:
3	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
4	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
5	chr14:24857849..24868599-chr14:24892485..24903992,27	MCF-7	breast:
6	chr14:24739150..24741254-chr14:24902393..24904882,2	MCF-7	breast:
7	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
8	chr14:24778683..24780646-chr14:24900996..24904566,3	K562	blood:
9	chr14:24707993..24709532-chr14:24903612..24905899,2	MCF-7	breast:
10	chr14:24656006..24657635-chr14:24902151..24905005,2	MCF-7	breast:
11	chr14:24769087..24772179-chr14:24900488..24904117,5	K562	blood:
12	chr14:24773182..24775572-chr14:24899600..24904217,4	MCF-7	breast:
13	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
14	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
15	chr14:24799476..24801488-chr14:24903490..24905098,2	K562	blood:
16	chr14:24808194..24811341-chr14:24902202..24904103,3	K562	blood:

No data

Variant related genes	Relation type
KHNYN	TF binding region
CBLN3	TF binding region
ENSG00000129465	Chromatin interaction
ENSG00000207141	Chromatin interaction
ENSG00000196943	Chromatin interaction
ENSG00000205978	Chromatin interaction
ENSG00000213906	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000136305	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10146759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11158709	1.00[CHB][hapmap]
rs11622667	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473723	1.00[CHB][hapmap]
rs1473724	1.00[CHB][hapmap]
rs1473726	1.00[CHB][hapmap]
rs1956891	1.00[CHB][hapmap]
rs1956892	1.00[CHB][hapmap]
rs1956894	1.00[CHB][hapmap]
rs1956895	1.00[CHB][hapmap]
rs1956897	1.00[CHB][hapmap]
rs2332332	1.00[CHB][hapmap]
rs4390517	1.00[CHB][hapmap]
rs4981515	1.00[CHB][hapmap]
rs4982915	1.00[CHB][hapmap]
rs4982922	1.00[CHB][hapmap]
rs4982923	1.00[CHB][hapmap]
rs4982924	1.00[CHB][hapmap]
rs4982925	1.00[CHB][hapmap]
rs4982926	1.00[CHB][hapmap]
rs7143047	1.00[CHB][hapmap]
rs7149255	1.00[CHB][hapmap]
rs8013354	1.00[CHB][hapmap]
rs911369	1.00[CHB][hapmap]
rs911370	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12891613	KIAA0323	Cis_1M	lymphoblastoid	RTeQTL
rs12891613	CBLN3	Cis_1M	lymphoblastoid	RTeQTL
rs12891613	THTPA	cis	cerebellum	SCAN
rs12891613	KHNYN	cis	lung	GTEx
rs12891613	OR4Q3	cis	cerebellum	SCAN
rs12891613	KIAA0323	cis	multi-tissue	Pritchard
rs12891613	KHNYN	cis	Whole Blood	GTEx
rs12891613	KHNYN	cis	cerebellum	SCAN
rs12891613	LOC643866	cis	multi-tissue	Pritchard
rs12891613	KHNYN	cis	parietal	SCAN
rs12891613	CBLN3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24900200-24906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:24900200-24911000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:24900600-24907800	Weak transcription	Small Intestine	intestine
4	chr14:24900600-24910600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr14:24901000-24905600	Weak transcription	Brain Angular Gyrus	brain
6	chr14:24901000-24906200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr14:24901000-24906600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr14:24901000-24906800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:24901000-24908600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:24901200-24904400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:24901200-24905800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr14:24901200-24906000	Strong transcription	Thymus	Thymus
13	chr14:24901400-24905800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr14:24901400-24906200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr14:24901400-24906400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr14:24901400-24906800	Weak transcription	K562	blood
17	chr14:24901400-24910200	Strong transcription	Aorta	Aorta
18	chr14:24901600-24904400	Strong transcription	Primary T cells from cord blood	blood
19	chr14:24901600-24904600	Strong transcription	Primary hematopoietic stem cells	blood
20	chr14:24901600-24904600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr14:24901600-24904800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr14:24901600-24905000	Strong transcription	Brain Anterior Caudate	brain
23	chr14:24901600-24905200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr14:24901600-24905400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr14:24901600-24905400	Strong transcription	Colonic Mucosa	Colon
26	chr14:24901600-24905400	Strong transcription	HepG2	liver
27	chr14:24901600-24905400	Strong transcription	HSMM	muscle
28	chr14:24901600-24905600	Strong transcription	Ovary	ovary
29	chr14:24901600-24905800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr14:24901600-24905800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr14:24901600-24905800	Strong transcription	Rectal Smooth Muscle	rectum
32	chr14:24901600-24906200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr14:24901600-24906200	Strong transcription	Lung	lung
34	chr14:24901600-24906800	Weak transcription	Fetal Brain Male	brain
35	chr14:24901600-24907200	Weak transcription	Hela-S3	cervix
36	chr14:24901600-24909800	Weak transcription	Fetal Heart	heart
37	chr14:24901600-24910400	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr14:24901800-24904200	Strong transcription	Left Ventricle	heart
39	chr14:24901800-24905200	Strong transcription	Primary B cells from cord blood	blood
40	chr14:24901800-24905200	Strong transcription	Fetal Kidney	kidney
41	chr14:24901800-24905200	Strong transcription	Fetal Muscle Leg	muscle
42	chr14:24901800-24905400	Strong transcription	Fetal Thymus	thymus
43	chr14:24901800-24905600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr14:24901800-24905600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr14:24901800-24909000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr14:24901800-24910000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr14:24902000-24904000	Strong transcription	Dnd41	blood
48	chr14:24902000-24904400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr14:24902000-24904400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr14:24902000-24905200	Strong transcription	Fetal Muscle Trunk	muscle

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