Variant report

Variant	rs4982917
Chromosome Location	chr14:24912755-24912756
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:24912707-24912786	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr14:24903683-24913003	HepG2	liver:	n/a	n/a
3	CHD1	chr14:24910986-24912822	IMR90	lung:	n/a	n/a
4	NFIC	chr14:24910940-24912945	HepG2	liver:	n/a	n/a
5	POLR2A	chr14:24912600-24912798	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr14:24910965-24912771	HCT-116	colon:	n/a	n/a
7	HEY1	chr14:24910553-24912767	HepG2	liver:	n/a	n/a
8	HCFC1	chr14:24910933-24912903	Hela-S3	cervix:	n/a	n/a
9	REST	chr14:24910904-24912790	H1-neurons	neurons:	n/a	chr14:24911331-24911340
10	POLR2A	chr14:24910786-24912868	HUVEC	blood vessel:	n/a	n/a
11	MAZ	chr14:24910712-24912758	IMR90	lung:	n/a	n/a
12	MAX	chr14:24910991-24912761	HepG2	liver:	n/a	n/a
13	TEAD4	chr14:24910495-24913064	HepG2	liver:	n/a	n/a
14	GABPA	chr14:24911215-24913044	MCF-7	breast:	n/a	chr14:24911992-24912003 chr14:24911992-24912006 chr14:24912044-24912058 chr14:24912047-24912058
15	MBD4	chr14:24910589-24912798	HepG2	liver:	n/a	n/a
16	MBD4	chr14:24910362-24912871	HepG2	liver:	n/a	n/a
17	MTA3	chr14:24910433-24912810	GM12878	blood:	n/a	n/a
18	POLR2A	chr14:24903965-24912834	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr14:24905748-24912859	GM12891	blood:	n/a	n/a
20	TBL1XR1	chr14:24912755-24912771	K562	blood:	n/a	n/a
21	CREB1	chr14:24910600-24912797	HepG2	liver:	n/a	n/a
22	MYBL2	chr14:24910814-24912973	HepG2	liver:	n/a	n/a
23	MYBL2	chr14:24910690-24913022	HepG2	liver:	n/a	n/a
24	POLR2A	chr14:24910609-24912893	SK-N-MC	brain:	n/a	n/a

No data

(count:12 , 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	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
5	chr14:24767332..24771774-chr14:24910139..24913002,7	MCF-7	breast:
6	chr14:24738849..24740758-chr14:24911753..24913964,2	MCF-7	breast:
7	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
8	chr14:24709335..24712189-chr14:24910783..24914037,3	K562	blood:
9	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
10	chr14:24767708..24770495-chr14:24910481..24913051,4	MCF-7	breast:
11	chr14:24740526..24742309-chr14:24912224..24913797,2	K562	blood:
12	chr14:24800598..24804207-chr14:24909756..24912911,5	K562	blood:

No data

Variant related genes	Relation type
SDR39U1	TF binding region
ENSG00000100949	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000196943	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000207141	Chromatin interaction
ENSG00000100968	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10083368	0.87[JPT][hapmap]
rs10083382	0.87[JPT][hapmap]
rs10083509	0.87[JPT][hapmap]
rs10129168	0.87[JPT][hapmap]
rs10133116	0.87[JPT][hapmap]
rs10133998	0.87[JPT][hapmap]
rs10140911	0.87[JPT][hapmap]
rs10143987	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1043831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158704	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158706	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158707	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621453	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621715	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626161	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627132	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11627137	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11628143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433369	1.00[ASN][1000 genomes]
rs12433402	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12879887	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12882878	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12884447	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12897925	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473725	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17103735	0.87[JPT][hapmap]
rs17103743	0.87[JPT][hapmap]
rs17103869	0.87[JPT][hapmap]
rs17103960	0.87[JPT][hapmap]
rs17104012	0.87[JPT][hapmap]
rs17184822	0.92[CEU][hapmap]
rs1951123	0.96[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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1956898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956899	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1956901	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956903	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277489	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2332333	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332334	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3211056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742521	0.86[JPT][hapmap]
rs3809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814810	0.85[JPT][hapmap]
rs4278673	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4290409	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4400972	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4433735	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4981518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981521	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981522	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981523	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981524	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982916	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982918	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4982919	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7142374	0.85[JPT][hapmap]
rs7143327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7144118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7148891	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7149743	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7151530	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7157349	0.85[JPT][hapmap]
rs737245	0.87[JPT][hapmap]
rs737246	0.87[JPT][hapmap]
rs737247	0.87[JPT][hapmap]
rs737248	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8008300	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8013991	0.83[ASN][1000 genomes]
rs8015535	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[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	nsv564061	chr14:24911138-24945331	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4982917	C14orf124	Cis_1M	lymphoblastoid	RTeQTL
rs4982917	SDR39U1	cis	Muscle Skeletal	GTEx
rs4982917	SDR39U1	cis	Skin Sun Exposed Lower leg	GTEx
rs4982917	SDR39U1	cis	Adipose Subcutaneous	GTEx
rs4982917	SDR39U1	cis	multi-tissue	Pritchard
rs4982917	SDR39U1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24910600-24913000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr14:24910800-24912800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:24910800-24913000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr14:24910800-24913000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr14:24910800-24913000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr14:24910800-24913200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr14:24911000-24912800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:24911000-24912800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:24911000-24912800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr14:24911000-24912800	Active TSS	Aorta	Aorta
11	chr14:24911000-24912800	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr14:24911000-24913000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr14:24911000-24913000	Active TSS	H1 Cell Line	embryonic stem cell
14	chr14:24911000-24913000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr14:24911000-24913000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:24911000-24913000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr14:24911000-24913000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr14:24911000-24913000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr14:24911000-24913000	Active TSS	Psoas Muscle	Psoas
20	chr14:24911000-24913000	Active TSS	A549	lung
21	chr14:24911000-24913000	Active TSS	NHLF	lung
22	chr14:24911000-24913200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr14:24911000-24913200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr14:24911000-24913200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr14:24911200-24912800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr14:24911200-24912800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr14:24911200-24912800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:24911200-24912800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr14:24911200-24912800	Active TSS	Lung	lung
30	chr14:24911200-24912800	Active TSS	HMEC	breast
31	chr14:24911200-24913000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:24911200-24913000	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr14:24911200-24913000	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr14:24911200-24913000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr14:24911200-24913200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr14:24911200-24913200	Active TSS	HSMM	muscle
37	chr14:24911400-24912800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr14:24911400-24912800	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr14:24911400-24912800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr14:24911400-24912800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr14:24911400-24912800	Active TSS	Esophagus	oesophagus
42	chr14:24911400-24912800	Active TSS	Fetal Intestine Small	intestine
43	chr14:24911400-24912800	Active TSS	Gastric	stomach
44	chr14:24911400-24912800	Active TSS	Left Ventricle	heart
45	chr14:24911400-24912800	Active TSS	Pancreas	Pancrea
46	chr14:24911400-24912800	Active TSS	Right Ventricle	heart
47	chr14:24911400-24912800	Active TSS	NHDF-Ad	bronchial
48	chr14:24911400-24912800	Active TSS	NHEK	skin
49	chr14:24911400-24913000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr14:24911400-24913000	Active TSS	Fetal Intestine Large	intestine

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