Variant report

Variant	rs2925140
Chromosome Location	chr17:18011358-18011359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18011044-18012845	U87	brain:	n/a	n/a
2	POLR2A	chr17:18011249-18011723	GM12891	blood:	n/a	n/a
3	POLR2A	chr17:18011139-18011868	GM12892	blood:	n/a	n/a
4	POLR2A	chr17:18011147-18012854	GM12892	blood:	n/a	n/a
5	POLR2A	chr17:18011352-18011444	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr17:18011280-18013634	K562	blood:	n/a	n/a
7	POLR2A	chr17:18011200-18011578	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr17:18011258-18013406	K562	blood:	n/a	n/a
9	POLR2A	chr17:18011236-18011697	GM12891	blood:	n/a	n/a
10	POLR2A	chr17:18011082-18013002	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr17:18011303-18011696	A549	lung:	n/a	n/a
12	POLR2A	chr17:18011048-18013298	GM12892	blood:	n/a	n/a
13	POLR2A	chr17:18011178-18011479	HCT-116	colon:	n/a	n/a
14	POLR2A	chr17:18011316-18011484	A549	lung:	n/a	n/a
15	POLR2A	chr17:18011161-18011865	K562	blood:	n/a	n/a
16	POLR2A	chr17:18010998-18012596	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr17:18011347-18011959	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr17:18010674-18012518	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr17:18011352-18013197	MCF-7	breast:	n/a	n/a
20	POLR2A	chr17:18010488-18014366	K562	blood:	n/a	n/a
21	POLR2A	chr17:18011286-18011418	GM12878	blood:	n/a	n/a
22	POLR2A	chr17:18011194-18011883	U87	brain:	n/a	n/a
23	POLR2A	chr17:18010725-18012712	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr17:18011305-18011896	U87	brain:	n/a	n/a
25	POLR2A	chr17:18010735-18015500	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr17:18011242-18012960	HepG2	liver:	n/a	n/a
27	POLR2A	chr17:18011308-18011504	HepG2	liver:	n/a	n/a
28	POLR2A	chr17:18010472-18015836	A549	lung:	n/a	n/a
29	POLR2A	chr17:18011303-18011812	GM12878	blood:	n/a	n/a
30	POLR2A	chr17:18011233-18011862	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr17:18011276-18011734	A549	lung:	n/a	n/a
32	POLR2A	chr17:18010593-18014325	HepG2	liver:	n/a	n/a
33	POLR2A	chr17:18011206-18011557	HepG2	liver:	n/a	n/a
34	POLR2A	chr17:18011222-18011949	GM12878	blood:	n/a	n/a
35	POLR2A	chr17:18011225-18011678	A549	lung:	n/a	n/a
36	POLR2A	chr17:18011281-18011791	GM12878	blood:	n/a	n/a
37	POLR2A	chr17:18011321-18011815	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr17:18010983-18014219	PFSK-1	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18004673..18008844-chr17:18009305..18012045,5	K562	blood:
2	chr17:18008952..18011744-chr17:18014672..18019225,4	MCF-7	breast:
3	chr17:17989884..17994353-chr17:18008301..18011863,4	MCF-7	breast:
4	chr17:18006973..18009716-chr17:18011197..18014211,3	MCF-7	breast:
5	chr17:18008903..18011616-chr17:18013439..18016712,4	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATPAF2-2	chr17:18009717-18011585	NONHSAT146144
2	lnc-ATPAF2-2	chr17:18009717-18011949	NONHSAT146145
3	lnc-ATPAF2-2	chr17:18010648-18013777	NONHSAT146149
4	lnc-ATPAF2-2	chr17:18009717-18014392	NONHSAT146147

No data

Variant related genes	Relation type
MYO15A	TF binding region
ENSG00000108591	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2272570	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925142	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2925143	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2955361	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955362	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955363	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955364	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2955374	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2955375	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955386	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2975000	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2975001	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2975002	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2975003	0.92[EUR][1000 genomes]
rs2975004	0.92[EUR][1000 genomes]
rs2975005	0.91[EUR][1000 genomes]
rs4513153	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925139	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502635	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7225972	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8077176	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv457697	chr17:18003845-18046290	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv574527	chr17:18003845-18046290	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2925140	ATPAF2	cis	Thyroid	GTEx
rs2925140	ATPAF2	cis	Heart Left Ventricle	GTEx
rs2925140	DRG2	cis	Artery Aorta	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17992200-18014000	Weak transcription	Right Atrium	heart
2	chr17:17993000-18012000	Strong transcription	Fetal Muscle Trunk	muscle
3	chr17:17994200-18011600	Strong transcription	Fetal Muscle Leg	muscle
4	chr17:17994200-18011800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr17:17994200-18012000	Strong transcription	Fetal Intestine Small	intestine
6	chr17:17994400-18011400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:17994600-18012800	Strong transcription	Thymus	Thymus
8	chr17:17995200-18011400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:17995200-18011400	Strong transcription	Lung	lung
10	chr17:17995200-18011400	Strong transcription	A549	lung
11	chr17:17995200-18011600	Strong transcription	Fetal Intestine Large	intestine
12	chr17:17995400-18011400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:17998000-18011600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:18002400-18019600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr17:18003000-18011800	Weak transcription	NHDF-Ad	bronchial
16	chr17:18003200-18021000	Weak transcription	Psoas Muscle	Psoas
17	chr17:18003400-18012400	Weak transcription	Hela-S3	cervix
18	chr17:18003800-18015200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr17:18004000-18012200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:18004200-18011800	Weak transcription	GM12878-XiMat	blood
21	chr17:18004800-18015400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr17:18005400-18012800	Weak transcription	Osteobl	bone
23	chr17:18005400-18013600	Weak transcription	HSMM	muscle
24	chr17:18005400-18017000	Weak transcription	HepG2	liver
25	chr17:18005600-18012200	Weak transcription	NH-A	brain
26	chr17:18005600-18015000	Weak transcription	HMEC	breast
27	chr17:18005800-18014800	Weak transcription	HSMMtube	muscle
28	chr17:18006400-18011600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr17:18006400-18011800	Strong transcription	Spleen	Spleen
30	chr17:18006800-18012800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr17:18007200-18011400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr17:18007200-18011800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr17:18007400-18011600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:18007600-18011600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:18007800-18011400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr17:18007800-18012400	Weak transcription	Left Ventricle	heart
37	chr17:18008200-18011600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr17:18008400-18012400	Weak transcription	Fetal Lung	lung
39	chr17:18009000-18015000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:18009600-18012400	Weak transcription	Colon Smooth Muscle	Colon
41	chr17:18009800-18011600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:18010000-18012200	Weak transcription	Brain Substantia Nigra	brain
43	chr17:18010200-18013000	Enhancers	Fetal Brain Male	brain
44	chr17:18010200-18014200	Genic enhancers	Liver	Liver
45	chr17:18010200-18015000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr17:18010400-18011400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr17:18010400-18012000	Weak transcription	Primary B cells from cord blood	blood
48	chr17:18010400-18012000	Weak transcription	Brain Angular Gyrus	brain
49	chr17:18010400-18012200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:18010400-18013000	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links