Variant report

Variant	rs62016939
Chromosome Location	chr15:50717042-50717043
allele	A/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	MAFK	chr15:50716234-50717079	Hela-S3	cervix:	n/a	n/a
2	CHD1	chr15:50716738-50717244	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr15:50716026-50717119	K562	blood:	n/a	n/a
4	POLR2A	chr15:50715922-50717154	K562	blood:	n/a	n/a
5	TCF12	chr15:50716108-50717097	ECC-1	luminal epithelium:	n/a	n/a
6	BCLAF1	chr15:50716120-50717068	GM12878	blood:	n/a	n/a
7	SRF	chr15:50715921-50717167	MCF-7	breast:	n/a	n/a
8	ZNF143	chr15:50716188-50717105	GM12878	blood:	n/a	n/a
9	PML	chr15:50715921-50717095	K562	blood:	n/a	chr15:50716396-50716404
10	HDAC2	chr15:50716069-50717061	MCF-7	breast:	n/a	chr15:50717024-50717038 chr15:50717025-50717039
11	ATF2	chr15:50716096-50717066	GM12878	blood:	n/a	chr15:50716544-50716558
12	PML	chr15:50715965-50717225	GM12878	blood:	n/a	chr15:50716396-50716404
13	MAX	chr15:50716024-50717248	MCF-7	breast:	n/a	n/a
14	CREB1	chr15:50716070-50717140	K562	blood:	n/a	n/a
15	POLR2A	chr15:50715425-50717621	GM12891	blood:	n/a	n/a
16	NR2F2	chr15:50715923-50717234	K562	blood:	n/a	n/a
17	ELF1	chr15:50715494-50717916	MCF-7	breast:	n/a	chr15:50716333-50716344 chr15:50716333-50716344 chr15:50717174-50717185 chr15:50717015-50717026 chr15:50716334-50716343 chr15:50716533-50716545 chr15:50717016-50717025 chr15:50717015-50717026
18	POLR2A	chr15:50715954-50717759	IMR90	lung:	n/a	n/a
19	MAZ	chr15:50715898-50717139	IMR90	lung:	n/a	n/a
20	MXI1	chr15:50715874-50717257	SK-N-SH	brain:	n/a	n/a
21	MYBL2	chr15:50715550-50717214	HepG2	liver:	n/a	n/a
22	POLR2A	chr15:50715464-50717416	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr15:50715962-50717145	H1-hESC	embryonic stem cell:	n/a	n/a
24	MXI1	chr15:50716202-50717329	GM12878	blood:	n/a	n/a
25	GABPA	chr15:50716086-50717148	SK-N-SH	brain:	n/a	n/a
26	MYC	chr15:50716078-50717060	K562	blood:	n/a	n/a
27	SRF	chr15:50716069-50717045	HCT-116	colon:	n/a	n/a
28	REST	chr15:50715920-50717266	H1-neurons	neurons:	n/a	chr15:50716814-50716834 chr15:50716348-50716361 chr15:50716462-50716475
29	CREB1	chr15:50716087-50717044	HepG2	liver:	n/a	n/a
30	POLR2A	chr15:50715925-50717189	PFSK-1	brain:	n/a	n/a
31	GABPA	chr15:50716054-50717140	SK-N-SH	brain:	n/a	n/a
32	CREB1	chr15:50716099-50717108	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:50716029-50717043	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr15:50715473-50717086	GM12878	blood:	n/a	n/a
35	SIN3A	chr15:50716142-50717621	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr15:50715245-50717511	HepG2	liver:	n/a	n/a
37	ZKSCAN1	chr15:50716169-50717042	Hela-S3	cervix:	n/a	n/a
38	RCOR1	chr15:50716153-50717095	K562	blood:	n/a	n/a
39	MAX	chr15:50716186-50717065	SK-N-SH	brain:	n/a	n/a
40	GABPA	chr15:50716087-50717224	A549	lung:	n/a	n/a
41	GABPA	chr15:50715789-50717432	MCF-7	breast:	n/a	n/a
42	TAF1	chr15:50716027-50717167	A549	lung:	n/a	n/a
43	ELF1	chr15:50715986-50717161	GM12878	blood:	n/a	chr15:50716333-50716344 chr15:50716333-50716344 chr15:50717015-50717026 chr15:50716334-50716343 chr15:50716533-50716545 chr15:50717016-50717025 chr15:50717015-50717026
44	TCF12	chr15:50715413-50717203	A549	lung:	n/a	chr15:50715646-50715653
45	REST	chr15:50715965-50717055	A549	lung:	n/a	chr15:50716814-50716834 chr15:50716348-50716361 chr15:50716462-50716475
46	YY1	chr15:50716163-50717081	GM12878	blood:	n/a	chr15:50716467-50716476
47	POLR2A	chr15:50715597-50717062	SK-N-MC	brain:	n/a	n/a
48	CREB1	chr15:50716049-50717120	HepG2	liver:	n/a	n/a
49	JUND	chr15:50716129-50717063	K562	blood:	n/a	n/a
50	SP1	chr15:50716012-50717108	A549	lung:	n/a	chr15:50716534-50716543 chr15:50716532-50716544 chr15:50716486-50716497 chr15:50716532-50716544 chr15:50716533-50716542 chr15:50716533-50716542 chr15:50716533-50716543 chr15:50716533-50716543 chr15:50716402-50716411

No.	Distal block	Cell Line	Cell type
1	chr1:161359042..161360035-chr15:50716770..50717404,2	Hela-S3	cervix:
2	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
3	chr15:50644601..50650486-chr15:50714318..50720349,10	K562	blood:
4	chr11:67777387..67778242-chr15:50716543..50717165,2	Hela-S3	cervix:
5	chr15:50714855..50718759-chr15:50728296..50731650,9	MCF-7	breast:
6	chr15:50644770..50653815-chr15:50713287..50720249,51	MCF-7	breast:
7	chr15:50716373..50717091-chr5:36606437..36607181,2	Hela-S3	cervix:
8	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
9	chr15:50647576..50648414-chr15:50716378..50717277,2	MCF-7	breast:
10	chr15:50715057..50718112-chr15:51199966..51202837,4	MCF-7	breast:
11	chr15:50716729..50717278-chr17:76837130..76837665,2	Hela-S3	cervix:
12	chr1:28975106..28975629-chr15:50716252..50717084,2	Hela-S3	cervix:
13	chr15:50716224..50718029-chr15:52121423..52123385,2	MCF-7	breast:

Variant related genes	Relation type
USP8	TF binding region
ENSG00000259715	Chromatin interaction
ENSG00000079215	Chromatin interaction
ENSG00000081014	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000006534	Chromatin interaction
ENSG00000264109	Chromatin interaction
ENSG00000055483	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000244879	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10519276	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519278	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070774	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070775	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070777	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070778	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070779	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070780	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070781	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070785	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11070786	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11070787	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11070788	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11630309	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11631351	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11631398	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11632697	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11632708	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11632823	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11633608	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11633624	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11633765	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11634832	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11637031	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11637104	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11637111	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11638198	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11638390	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12439248	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12440152	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17519466	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17519536	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17597852	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17597915	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17598061	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414044	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414045	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34659874	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4380013	0.84[EUR][1000 genomes]
rs4774569	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774570	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774571	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774572	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775883	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775884	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775885	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775886	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775888	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775889	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62016938	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016940	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016942	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016943	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016944	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019074	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019075	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019076	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019077	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019078	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62019079	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019080	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019082	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019084	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019085	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019087	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62019112	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62019113	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62019115	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62019116	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62019117	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7165464	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168783	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7169778	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7170114	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7181536	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7182569	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182980	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7494907	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8030373	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8037446	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8037553	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs934636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv904210	chr15:50702058-50786024	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1040717	chr15:50715572-50846521	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50715600-50717200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:50715600-50717200	Active TSS	Duodenum Mucosa	Duodenum
3	chr15:50715600-50717200	Active TSS	Stomach Smooth Muscle	stomach
4	chr15:50715600-50717400	Active TSS	NH-A	brain
5	chr15:50715600-50717400	Active TSS	NHEK	skin
6	chr15:50715600-50717600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:50715600-50718000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr15:50715600-50718400	Active TSS	Hela-S3	cervix
9	chr15:50715800-50717200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:50715800-50717200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:50715800-50717200	Active TSS	Brain Angular Gyrus	brain
12	chr15:50715800-50717200	Active TSS	Brain Hippocampus Middle	brain
13	chr15:50715800-50717200	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr15:50715800-50717200	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr15:50715800-50717200	Active TSS	Rectal Smooth Muscle	rectum
16	chr15:50715800-50717400	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr15:50715800-50717400	Active TSS	Brain Anterior Caudate	brain
18	chr15:50715800-50717400	Active TSS	Brain Cingulate Gyrus	brain
19	chr15:50715800-50717400	Active TSS	Colon Smooth Muscle	Colon
20	chr15:50715800-50717400	Active TSS	Fetal Brain Female	brain
21	chr15:50715800-50717400	Active TSS	Thymus	Thymus
22	chr15:50715800-50717600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:50715800-50717600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:50715800-50717600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:50715800-50717800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr15:50715800-50717800	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr15:50715800-50717800	Active TSS	HSMM	muscle
28	chr15:50715800-50717800	Active TSS	HSMMtube	muscle
29	chr15:50715800-50718000	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr15:50715800-50718000	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr15:50715800-50718200	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr15:50715800-50718200	Active TSS	Colonic Mucosa	Colon
33	chr15:50715800-50718200	Active TSS	Right Atrium	heart
34	chr15:50715800-50718400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:50715800-50718400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:50715800-50718400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:50716000-50717200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr15:50716000-50717200	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr15:50716000-50717200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr15:50716000-50717200	Active TSS	Fetal Heart	heart
41	chr15:50716000-50717200	Active TSS	Fetal Stomach	stomach
42	chr15:50716000-50717200	Active TSS	Placenta Amnion	Placenta Amnion
43	chr15:50716000-50717200	Active TSS	HUVEC	blood vessel
44	chr15:50716000-50717400	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr15:50716000-50717400	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr15:50716000-50717400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:50716000-50717400	Active TSS	Aorta	Aorta
48	chr15:50716000-50717400	Active TSS	Fetal Kidney	kidney
49	chr15:50716000-50717400	Active TSS	Pancreas	Pancrea
50	chr15:50716000-50717400	Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links