Variant report

Variant	rs927292
Chromosome Location	chr14:69258841-69258842
allele	C/G
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	NFIC	chr14:69258747-69263739	GM12878	blood:	n/a	n/a
2	POLR2A	chr14:69250963-69263207	U87	brain:	n/a	n/a
3	BRCA1	chr14:69258561-69259147	H1-hESC	embryonic stem cell:	n/a	chr14:69259009-69259018
4	CHD2	chr14:69258147-69259199	H1-hESC	embryonic stem cell:	n/a	chr14:69258897-69258907 chr14:69258373-69258383 chr14:69259118-69259128
5	PBX3	chr14:69258047-69262185	A549	lung:	n/a	n/a
6	RELA	chr14:69258539-69263496	GM12891	blood:	n/a	n/a
7	POLR2A	chr14:69258369-69259894	GM12891	blood:	n/a	n/a
8	POLR2A	chr14:69254988-69263278	GM12892	blood:	n/a	n/a
9	POLR2A	chr14:69255614-69263201	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr14:69254928-69263445	GM12892	blood:	n/a	n/a
11	EP300	chr14:69258805-69263522	ECC-1	luminal epithelium:	n/a	chr14:69260104-69260120 chr14:69260038-69260052 chr14:69261261-69261270 chr14:69260641-69260657 chr14:69259995-69260009 chr14:69260648-69260657
12	POLR2A	chr14:69257221-69263637	MCF10A-Er-Src	breast:	n/a	n/a
13	MTA3	chr14:69254975-69264454	GM12878	blood:	n/a	n/a
14	POLR2A	chr14:69257126-69263442	GM12891	blood:	n/a	n/a
15	HDAC2	chr14:69257848-69261541	MCF-7	breast:	n/a	chr14:69260034-69260048 chr14:69260037-69260051 chr14:69260032-69260046 chr14:69260036-69260050 chr14:69258035-69258049 chr14:69260118-69260127 chr14:69260038-69260052 chr14:69258424-69258438 chr14:69260039-69260053 chr14:69260035-69260049 chr14:69258425-69258439
16	FOXM1	chr14:69257771-69260503	MCF-7	breast:	n/a	n/a
17	POLR2A	chr14:69258806-69259881	GM12878	blood:	n/a	n/a
18	POLR2A	chr14:69256736-69263833	Raji	blood:	n/a	n/a
19	POLR2A	chr14:69255146-69263257	GM18526	blood:	n/a	n/a
20	SIN3AK20	chr14:69258284-69258938	A549	lung:	n/a	n/a
21	HEY1	chr14:69257251-69263120	HepG2	liver:	n/a	chr14:69260559-69260574 chr14:69260178-69260187 chr14:69260176-69260185
22	NFATC1	chr14:69255663-69260669	GM12878	blood:	n/a	n/a
23	POLR2A	chr14:69258790-69262017	HepG2	liver:	n/a	n/a
24	POLR2A	chr14:69252481-69263392	GM18505	blood:	n/a	n/a
25	MAX	chr14:69258724-69261645	HepG2	liver:	n/a	n/a
26	STAT5A	chr14:69257966-69260119	GM12878	blood:	n/a	chr14:69259835-69259847 chr14:69258037-69258048 chr14:69259312-69259324 chr14:69259829-69259841 chr14:69259935-69259947 chr14:69259443-69259451 chr14:69258897-69258909 chr14:69258124-69258135
27	SIN3AK20	chr14:69258813-69260467	H1-hESC	embryonic stem cell:	n/a	n/a
28	CHD2	chr14:69258414-69263620	Hela-S3	cervix:	n/a	chr14:69258897-69258907 chr14:69261411-69261421 chr14:69259834-69259844 chr14:69261032-69261042 chr14:69259118-69259128
29	POLR2A	chr14:69258734-69259522	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr14:69250890-69259922	A549	lung:	n/a	n/a
31	ELF1	chr14:69258787-69261410	GM12878	blood:	n/a	chr14:69261213-69261222
32	REST	chr14:69258652-69259869	A549	lung:	n/a	chr14:69259118-69259128 chr14:69259269-69259277
33	POLR2A	chr14:69258329-69262795	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr14:69254922-69263025	HUVEC	blood vessel:	n/a	n/a
35	CHD2	chr14:69258833-69259214	HepG2	liver:	n/a	chr14:69258897-69258907 chr14:69259118-69259128
36	BCL3	chr14:69255275-69258942	A549	lung:	n/a	n/a
37	RUNX3	chr14:69256419-69263509	GM12878	blood:	n/a	n/a
38	POLR2A	chr14:69251221-69263347	U87	brain:	n/a	n/a
39	POLR2A	chr14:69256682-69263552	HepG2	liver:	n/a	n/a
40	POLR2A	chr14:69255405-69263158	MCF-7	breast:	n/a	n/a
41	POLR2A	chr14:69254889-69263164	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr14:69255690-69263291	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr14:69255224-69263246	GM19193	blood:	n/a	n/a
44	POLR2A	chr14:69257288-69264495	PBDE	blood:	n/a	n/a
45	POLR2A	chr14:69258798-69263153	K562	blood:	n/a	n/a
46	BCLAF1	chr14:69258400-69259924	GM12878	blood:	n/a	chr14:69259582-69259591 chr14:69259334-69259347
47	POLR2A	chr14:69255652-69261985	HCT-116	colon:	n/a	n/a
48	TBP	chr14:69258714-69260570	K562	blood:	n/a	n/a
49	TAF1	chr14:69258364-69260769	MCF-7	breast:	n/a	n/a
50	POLR2A	chr14:69255300-69263602	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:69090615..69103406-chr14:69249821..69264188,29	MCF-7	breast:
2	chr14:69235719..69238607-chr14:69258335..69259856,2	MCF-7	breast:
3	chr14:68915233..68917700-chr14:69258123..69259734,2	K562	blood:
4	chr14:69258569..69259287-chr16:13548283..13549013,2	HCT-116	colon:
5	chr14:68350452..68352881-chr14:69258194..69261622,3	MCF-7	breast:
6	chr14:68930492..68947840-chr14:69251918..69264148,62	MCF-7	breast:
7	chr14:69149566..69152941-chr14:69256310..69260478,3	MCF-7	breast:
8	chr14:68282145..68286888-chr14:69256784..69261104,5	MCF-7	breast:
9	chr14:69257700..69260072-chr17:1618563..1621459,2	MCF-7	breast:
10	chr14:69091753..69104091-chr14:69256141..69263760,20	MCF-7	breast:
11	chr14:69258203..69260706-chr17:56707780..56709362,2	MCF-7	breast:
12	chr14:68352272..68355022-chr14:69258244..69262334,3	MCF-7	breast:
13	chr12:69004642..69006364-chr14:69258588..69260544,2	MCF-7	breast:
14	chr14:69258720..69263996-chr17:57918463..57922385,5	MCF-7	breast:
15	chr14:69258435..69258964-chr3:150480744..150481394,2	Hela-S3	cervix:
16	chr14:69208318..69211269-chr14:69258281..69259846,2	MCF-7	breast:
17	chr14:55595591..55597639-chr14:69257922..69259895,2	MCF-7	breast:

Variant related genes	Relation type
ZFP36L1	TF binding region
ENSG00000199004	Chromatin interaction
ENSG00000072121	Chromatin interaction
ENSG00000181788	Chromatin interaction
ENSG00000259038	Chromatin interaction
ENSG00000186594	Chromatin interaction
ENSG00000167716	Chromatin interaction
ENSG00000131981	Chromatin interaction
ENSG00000182185	Chromatin interaction
ENSG00000258623	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000127314	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10142466	0.87[ASN][1000 genomes]
rs11158762	0.81[JPT][hapmap]
rs11626883	0.87[ASN][1000 genomes]
rs12889006	0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1465788	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1595260	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1595261	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17106304	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17835641	0.87[ASN][1000 genomes]
rs17835647	0.87[ASN][1000 genomes]
rs1836984	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs194748	0.94[ASN][1000 genomes]
rs194749	0.89[ASN][1000 genomes]
rs194751	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs194778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2236262	0.87[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs2236263	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34489253	0.90[ASN][1000 genomes]
rs367677	0.91[ASN][1000 genomes]
rs3742887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825568	0.87[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4899258	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4899259	0.94[ASN][1000 genomes]
rs4902651	0.87[ASN][1000 genomes]
rs6573857	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7146217	0.88[JPT][hapmap];0.88[YRI][hapmap]
rs7149271	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7156516	0.94[ASN][1000 genomes]
rs8011558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8022092	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035267	chr14:69230254-69348126	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv542123	chr14:69230254-69348126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv902070	chr14:69244214-69308182	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs927292	ZFP36L1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69253800-69259800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
2	chr14:69254000-69259600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
3	chr14:69254200-69259600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
4	chr14:69254200-69259600	Transcr. at gene 5' and 3'	Fetal Lung	lung
5	chr14:69254200-69259800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr14:69255000-69259200	Transcr. at gene 5' and 3'	HSMM	muscle
7	chr14:69255000-69259600	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
8	chr14:69255000-69259800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:69255000-69260400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr14:69255000-69262400	Active TSS	Right Atrium	heart
11	chr14:69255200-69259000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:69255200-69259400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
13	chr14:69255400-69259000	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
14	chr14:69255400-69259400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr14:69255400-69259400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
16	chr14:69255400-69259800	Transcr. at gene 5' and 3'	NHEK	skin
17	chr14:69255400-69263200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr14:69255800-69259200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr14:69255800-69259400	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
20	chr14:69255800-69259600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
21	chr14:69255800-69259800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
22	chr14:69256000-69259200	Transcr. at gene 5' and 3'	Stomach Mucosa	stomach
23	chr14:69256200-69263000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr14:69256400-69259600	Active TSS	Brain Anterior Caudate	brain
25	chr14:69256400-69263200	Active TSS	Primary T cells from cord blood	blood
26	chr14:69256600-69260600	Active TSS	NH-A	brain
27	chr14:69256600-69263000	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr14:69256800-69259800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
29	chr14:69256800-69260800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr14:69256800-69263200	Active TSS	Small Intestine	intestine
31	chr14:69257000-69260400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr14:69257000-69260800	Active TSS	HSMMtube	muscle
33	chr14:69257200-69259600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr14:69257200-69259800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr14:69257200-69261400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr14:69257200-69263200	Active TSS	Aorta	Aorta
37	chr14:69257200-69263400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr14:69257200-69263600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
39	chr14:69257200-69263800	Active TSS	H9 Cell Line	embryonic stem cell
40	chr14:69257400-69259600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr14:69257400-69259800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr14:69257400-69260800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr14:69257400-69260800	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr14:69257400-69261200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
45	chr14:69257400-69262800	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr14:69257400-69263000	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr14:69257400-69263200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr14:69257400-69263200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:69257400-69263200	Active TSS	Ovary	ovary
50	chr14:69257400-69263200	Active TSS	Spleen	Spleen

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