Variant report

Variant	rs11158704
Chromosome Location	chr14:24911116-24911117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:114)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:114 , 50 per page) page: 1 2 3

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	chr14:24911115-24912468	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr14:24911100-24911250	HPAF	blood vessel:	n/a	n/a
4	GABPA	chr14:24911063-24912610	MCF-7	breast:	n/a	chr14:24911992-24912003 chr14:24911992-24912006 chr14:24912044-24912058 chr14:24912047-24912058
5	POLR2A	chr14:24911084-24912401	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr14:24910478-24912449	Hela-S3	cervix:	n/a	n/a
7	JUND	chr14:24911070-24912454	HepG2	liver:	n/a	n/a
8	POLR2A	chr14:24905485-24912569	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr14:24910801-24912429	U87	brain:	n/a	n/a
10	POLR2A	chr14:24905933-24912504	MCF-7	breast:	n/a	n/a
11	MAX	chr14:24910938-24912435	HCT-116	colon:	n/a	n/a
12	POLR2A	chr14:24911044-24912459	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr14:24911091-24912283	Gliobla	brain:	n/a	n/a
14	HDAC2	chr14:24911090-24912456	HepG2	liver:	n/a	n/a
15	POLR2A	chr14:24903683-24913003	HepG2	liver:	n/a	n/a
16	POLR2A	chr14:24911022-24912428	GM12892	blood:	n/a	n/a
17	MAZ	chr14:24911115-24912339	HepG2	liver:	n/a	n/a
18	POLR2A	chr14:24905442-24912440	HepG2	liver:	n/a	n/a
19	POLR2A	chr14:24910917-24912589	HUVEC	blood vessel:	n/a	n/a
20	KAP1	chr14:24911047-24912392	U2OS	brain:	n/a	n/a
21	CHD1	chr14:24910986-24912822	IMR90	lung:	n/a	n/a
22	NFIC	chr14:24910940-24912945	HepG2	liver:	n/a	n/a
23	MAX	chr14:24911021-24912418	MCF-7	breast:	n/a	n/a
24	POLR2A	chr14:24903880-24912404	K562	blood:	n/a	n/a
25	POLR2A	chr14:24911109-24912367	H1-hESC	embryonic stem cell:	n/a	n/a
26	IRF1	chr14:24911013-24912422	K562	blood:	n/a	n/a
27	POLR2A	chr14:24910760-24912648	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr14:24909511-24912466	HCT-116	colon:	n/a	n/a
29	POLR2A	chr14:24905283-24912400	Hela-S3	cervix:	n/a	n/a
30	MAX	chr14:24910965-24912771	HCT-116	colon:	n/a	n/a
31	HEY1	chr14:24910553-24912767	HepG2	liver:	n/a	n/a
32	NFATC1	chr14:24910555-24911608	GM12878	blood:	n/a	n/a
33	TAF1	chr14:24911088-24912371	H1-neurons	neurons:	n/a	n/a
34	HCFC1	chr14:24910933-24912903	Hela-S3	cervix:	n/a	n/a
35	MAX	chr14:24911001-24912431	A549	lung:	n/a	n/a
36	REST	chr14:24910904-24912790	H1-neurons	neurons:	n/a	chr14:24911331-24911340
37	POLR2A	chr14:24911084-24912419	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr14:24910462-24912424	HUVEC	blood vessel:	n/a	n/a
39	MAX	chr14:24911085-24912377	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr14:24910786-24912868	HUVEC	blood vessel:	n/a	n/a
41	EP300	chr14:24911002-24912406	HepG2	liver:	n/a	n/a
42	POLR2A	chr14:24910454-24912726	HepG2	liver:	n/a	n/a
43	MAZ	chr14:24910712-24912758	IMR90	lung:	n/a	n/a
44	POLR2A	chr14:24910513-24912438	Hela-S3	cervix:	n/a	n/a
45	MTA3	chr14:24911025-24912418	GM12878	blood:	n/a	n/a
46	POLR2A	chr14:24905921-24912469	GM12878	blood:	n/a	n/a
47	NR2F2	chr14:24911063-24912425	MCF-7	breast:	n/a	n/a
48	POLR2A	chr14:24905513-24912697	GM12878	blood:	n/a	n/a
49	POLR2A	chr14:24910952-24912636	GM12878	blood:	n/a	n/a
50	MAX	chr14:24910991-24912761	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:24836714..24839783-chr14:24910555..24913487,3	K562	blood:
2	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
3	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
4	chr14:24562331..24564529-chr14:24910345..24912043,2	K562	blood:
5	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
6	chr14:24911102..24911676-chr2:101924903..101925680,2	Hela-S3	cervix:
7	chr14:24767332..24771774-chr14:24910139..24913002,7	MCF-7	breast:
8	chr14:24796552..24799266-chr14:24908909..24911628,3	K562	blood:
9	chr14:24910782..24911552-chr4:71858996..71859672,2	Hela-S3	cervix:
10	chr14:24698279..24701346-chr14:24909291..24912292,3	MCF-7	breast:
11	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
12	chr14:24909605..24912144-chr17:56736218..56737898,2	MCF-7	breast:
13	chr14:24709335..24712189-chr14:24910783..24914037,3	K562	blood:
14	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
15	chr14:24767708..24770495-chr14:24910481..24913051,4	MCF-7	breast:
16	chr14:24800598..24804207-chr14:24909756..24912911,5	K562	blood:

No data

Variant related genes	Relation type
SDR39U1	TF binding region
ENSG00000213903	Chromatin interaction
ENSG00000156136	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000207141	Chromatin interaction
ENSG00000196943	Chromatin interaction
ENSG00000163162	Chromatin interaction
ENSG00000100889	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000129535	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000100968	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10143987	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1043831	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043839	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158706	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158707	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621453	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621715	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626161	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627132	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11627137	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11628143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433369	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12433402	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12879887	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12882878	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12884447	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12897925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473725	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1951123	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956893	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1956896	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1956898	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956899	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1956901	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956903	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956904	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273628	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277489	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2332333	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332334	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3211056	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4278673	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4290409	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4400972	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4433735	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4981518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981521	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981522	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981523	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981524	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982913	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982914	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982917	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982918	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4982919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982920	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7143327	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7144118	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7148891	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7149743	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7151530	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs737248	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8008300	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8013991	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs8015535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966493	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv1053330	chr14:24908047-24993666	Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	n/a
4	nsv482171	chr14:24908974-24912007	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	40 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11158704	SDR39U1	cis	Whole Blood	GTEx
rs11158704	SDR39U1	cis	Muscle Skeletal	GTEx
rs11158704	C14orf124	Cis_1M	lymphoblastoid	RTeQTL
rs11158704	SDR39U1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24908800-24911200	Weak transcription	Ovary	ovary
2	chr14:24909800-24911200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:24909800-24911200	Enhancers	Stomach Mucosa	stomach
4	chr14:24910400-24911200	Weak transcription	Gastric	stomach
5	chr14:24910400-24911200	Weak transcription	Lung	lung
6	chr14:24910400-24911200	Flanking Active TSS	HMEC	breast
7	chr14:24910400-24911400	Enhancers	Spleen	Spleen
8	chr14:24910600-24911200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:24910600-24911200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr14:24910600-24911200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr14:24910600-24911200	Transcr. at gene 5' and 3'	HSMM	muscle
12	chr14:24910600-24911400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:24910600-24911400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr14:24910600-24911400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr14:24910600-24911400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr14:24910600-24911400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr14:24910600-24911400	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr14:24910600-24911400	Flanking Active TSS	GM12878-XiMat	blood
19	chr14:24910600-24911400	Flanking Active TSS	HUVEC	blood vessel
20	chr14:24910600-24911400	Flanking Active TSS	K562	blood
21	chr14:24910600-24913000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr14:24910800-24911200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr14:24910800-24911200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:24910800-24911200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr14:24910800-24911200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr14:24910800-24911200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr14:24910800-24911200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:24910800-24911200	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr14:24910800-24911200	Enhancers	Esophagus	oesophagus
30	chr14:24910800-24911200	Flanking Active TSS	Fetal Brain Male	brain
31	chr14:24910800-24911200	Flanking Active TSS	NH-A	brain
32	chr14:24910800-24911200	Flanking Active TSS	Osteobl	bone
33	chr14:24910800-24911400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:24910800-24911400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr14:24910800-24911400	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr14:24910800-24911400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr14:24910800-24911400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr14:24910800-24911400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr14:24910800-24911400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr14:24910800-24911400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr14:24910800-24911400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr14:24910800-24911400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr14:24910800-24911400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr14:24910800-24911400	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr14:24910800-24911400	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr14:24910800-24911400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr14:24910800-24911400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr14:24910800-24911400	Enhancers	Small Intestine	intestine
49	chr14:24910800-24911400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
50	chr14:24910800-24911400	Flanking Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links