Variant report

Variant	rs4902683
Chromosome Location	chr14:69442848-69442849
allele	C/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	HNF4G	chr14:69442709-69443262	HepG2	liver:	n/a	chr14:69443042-69443054 chr14:69443041-69443056 chr14:69443041-69443054
2	HDAC2	chr14:69442764-69443484	HepG2	liver:	n/a	n/a
3	RXRA	chr14:69442787-69443182	HepG2	liver:	n/a	n/a
4	POLR2A	chr14:69442166-69443097	U87	brain:	n/a	n/a
5	BRCA1	chr14:69442725-69442962	HepG2	liver:	n/a	n/a
6	POLR2A	chr14:69441718-69446518	HepG2	liver:	n/a	n/a
7	MXI1	chr14:69441660-69447416	IMR90	lung:	n/a	n/a
8	CHD1	chr14:69441180-69450261	IMR90	lung:	n/a	chr14:69446695-69446705
9	MYBL2	chr14:69442809-69443276	HepG2	liver:	n/a	n/a
10	MBD4	chr14:69442731-69443358	HepG2	liver:	n/a	n/a
11	HEY1	chr14:69442787-69443378	HepG2	liver:	n/a	n/a
12	MAX	chr14:69442257-69443651	HepG2	liver:	n/a	chr14:69442450-69442457 chr14:69442448-69442459 chr14:69442447-69442460 chr14:69442449-69442459 chr14:69442449-69442458
13	MAZ	chr14:69442284-69447004	IMR90	lung:	n/a	chr14:69442450-69442457 chr14:69442448-69442459 chr14:69446258-69446267 chr14:69446222-69446232 chr14:69442447-69442460 chr14:69444518-69444528 chr14:69445035-69445045 chr14:69442449-69442459 chr14:69445545-69445555 chr14:69446056-69446066 chr14:69445647-69445657 chr14:69446420-69446430 chr14:69442449-69442458
14	POLR2A	chr14:69442813-69443284	HepG2	liver:	n/a	n/a
15	POLR2A	chr14:69442290-69443666	HepG2	liver:	n/a	n/a
16	POLR2A	chr14:69441592-69445621	HUVEC	blood vessel:	n/a	n/a
17	SP1	chr14:69442716-69443333	HepG2	liver:	n/a	chr14:69443305-69443315 chr14:69443063-69443072 chr14:69443305-69443314 chr14:69443062-69443071 chr14:69443061-69443073 chr14:69443305-69443314 chr14:69443002-69443016 chr14:69443062-69443072
18	POLR2A	chr14:69442814-69443586	HepG2	liver:	n/a	n/a
19	EP300	chr14:69442758-69443342	HepG2	liver:	n/a	chr14:69442994-69443007
20	ZNF263	chr14:69442769-69443343	HEK293-T-REx	kidney:	n/a	chr14:69442972-69442993 chr14:69442994-69443015
21	POLR2A	chr14:69442829-69443157	H1-hESC	embryonic stem cell:	n/a	n/a
22	HNF4A	chr14:69442735-69443274	HepG2	liver:	n/a	chr14:69443040-69443055 chr14:69443042-69443054 chr14:69443041-69443054
23	FOXA1	chr14:69442808-69443329	HepG2	liver:	n/a	chr14:69443231-69443243
24	HNF4G	chr14:69442709-69443376	HepG2	liver:	n/a	chr14:69443042-69443054 chr14:69443041-69443056 chr14:69443041-69443054
25	HNF4A	chr14:69442822-69443311	HepG2	liver:	n/a	chr14:69443040-69443055 chr14:69443042-69443054 chr14:69443041-69443054
26	MYBL2	chr14:69442710-69443416	HepG2	liver:	n/a	n/a
27	MAX	chr14:69442735-69443701	HepG2	liver:	n/a	n/a
28	MXI1	chr14:69442097-69447256	SK-N-SH	brain:	n/a	n/a
29	HNF4A	chr14:69442825-69443230	HepG2	liver:	n/a	chr14:69443040-69443055 chr14:69443042-69443054 chr14:69443041-69443054
30	POLR2A	chr14:69442571-69447283	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr14:69441290-69449923	IMR90	lung:	n/a	n/a
32	POLR2A	chr14:69441164-69443163	U87	brain:	n/a	n/a
33	POLR2A	chr14:69442232-69447465	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:69403117..69416483-chr14:69441657..69449888,50	MCF-7	breast:
2	chr14:69441561..69443821-chr6:122931001..122932824,2	MCF-7	breast:
3	chr14:69442323..69443910-chr14:69472341..69473881,2	MCF-7	breast:
4	chr14:69441449..69443783-chr14:69546294..69548091,2	K562	blood:
5	chr14:69261314..69263006-chr14:69442785..69445190,2	MCF-7	breast:
6	chr14:69441719..69443220-chr14:69520758..69522938,2	MCF-7	breast:
7	chr14:69402982..69422523-chr14:69436263..69448017,46	MCF-7	breast:
8	chr14:69442124..69444502-chr20:46130530..46133122,2	MCF-7	breast:

Variant related genes	Relation type
ACTN1-AS1	TF binding region
ENSG00000124151	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000135549	Chromatin interaction
ENSG00000258531	Chromatin interaction
ENSG00000072110	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10151419	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11620980	1.00[ASN][1000 genomes]
rs11623192	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1275194	0.95[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983700	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2012752	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242091	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242096	1.00[ASN][1000 genomes]
rs242097	0.95[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242099	1.00[ASN][1000 genomes]
rs242100	0.82[MEX][hapmap]
rs242101	0.84[EUR][1000 genomes]
rs242102	0.95[CEU][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242104	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs242109	0.95[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs398504	1.00[ASN][1000 genomes]
rs4083451	1.00[ASN][1000 genomes]
rs436106	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899275	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902681	1.00[ASN][1000 genomes]
rs56060157	1.00[ASN][1000 genomes]
rs61981591	1.00[ASN][1000 genomes]
rs761898	0.82[MEX][hapmap]
rs927064	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4902683	MAP3K9	cis	cerebellum	SCAN
rs4902683	GALNTL1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69428600-69443400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:69429400-69443800	Weak transcription	Brain Germinal Matrix	brain
3	chr14:69431800-69444000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
4	chr14:69432600-69443000	Weak transcription	Brain Substantia Nigra	brain
5	chr14:69437000-69443000	Weak transcription	Fetal Brain Male	brain
6	chr14:69437800-69443600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr14:69438200-69443200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:69438400-69444400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:69438600-69443000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:69438800-69443000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr14:69438800-69443400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr14:69438800-69444000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:69439000-69443600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr14:69439200-69444400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
15	chr14:69439400-69443400	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr14:69440400-69443400	Transcr. at gene 5' and 3'	NHLF	lung
17	chr14:69440600-69443000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr14:69440600-69443400	Enhancers	Colonic Mucosa	Colon
19	chr14:69440600-69444000	Enhancers	Stomach Mucosa	stomach
20	chr14:69440600-69444400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr14:69440800-69443200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:69440800-69443600	Enhancers	Right Ventricle	heart
23	chr14:69441000-69443000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr14:69441000-69443400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr14:69441200-69443000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:69441200-69443400	Genic enhancers	Fetal Intestine Small	intestine
27	chr14:69441200-69443400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr14:69441200-69443800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr14:69441200-69444000	Enhancers	Left Ventricle	heart
30	chr14:69441200-69444200	Transcr. at gene 5' and 3'	NHEK	skin
31	chr14:69441200-69445200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:69441400-69443000	Genic enhancers	Primary T cells from cord blood	blood
33	chr14:69441400-69443000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr14:69441400-69443000	Genic enhancers	Hela-S3	cervix
35	chr14:69441400-69443600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr14:69441400-69443800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr14:69441400-69444400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr14:69441600-69443200	Enhancers	Adipose Nuclei	Adipose
39	chr14:69441600-69443200	Transcr. at gene 5' and 3'	HSMM	muscle
40	chr14:69441600-69443400	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr14:69441600-69443400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr14:69441600-69443400	Enhancers	Liver	Liver
43	chr14:69441600-69443400	Enhancers	Pancreas	Pancrea
44	chr14:69441600-69443600	Enhancers	Ovary	ovary
45	chr14:69441600-69443800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr14:69441600-69444000	Enhancers	Fetal Thymus	thymus
47	chr14:69441600-69444200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr14:69441600-69444400	Transcr. at gene 5' and 3'	HMEC	breast
49	chr14:69441800-69443000	Weak transcription	Small Intestine	intestine
50	chr14:69441800-69443400	Genic enhancers	H9 Cell Line	embryonic stem cell

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