Variant report

Variant	rs854764
Chromosome Location	chr17:18011750-18011751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 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	chr17:18011139-18011868	GM12892	blood:	n/a	n/a
3	POLR2A	chr17:18011147-18012854	GM12892	blood:	n/a	n/a
4	POLR2A	chr17:18011280-18013634	K562	blood:	n/a	n/a
5	POLR2A	chr17:18011258-18013406	K562	blood:	n/a	n/a
6	POLR2A	chr17:18011082-18013002	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr17:18011048-18013298	GM12892	blood:	n/a	n/a
8	POLR2A	chr17:18011161-18011865	K562	blood:	n/a	n/a
9	POLR2A	chr17:18010998-18012596	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr17:18011347-18011959	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr17:18010674-18012518	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr17:18011375-18011896	U87	brain:	n/a	n/a
13	POLR2A	chr17:18011352-18013197	MCF-7	breast:	n/a	n/a
14	POLR2A	chr17:18010488-18014366	K562	blood:	n/a	n/a
15	POLR2A	chr17:18011194-18011883	U87	brain:	n/a	n/a
16	POLR2A	chr17:18010725-18012712	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr17:18011305-18011896	U87	brain:	n/a	n/a
18	POLR2A	chr17:18010735-18015500	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr17:18011242-18012960	HepG2	liver:	n/a	n/a
20	POLR2A	chr17:18010472-18015836	A549	lung:	n/a	n/a
21	POLR2A	chr17:18011303-18011812	GM12878	blood:	n/a	n/a
22	POLR2A	chr17:18011233-18011862	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr17:18010593-18014325	HepG2	liver:	n/a	n/a
24	POLR2A	chr17:18011222-18011949	GM12878	blood:	n/a	n/a
25	POLR2A	chr17:18011281-18011791	GM12878	blood:	n/a	n/a
26	POLR2A	chr17:18011690-18012264	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr17:18011503-18012613	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr17:18011321-18011815	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr17:18010983-18014219	PFSK-1	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:18004673..18008844-chr17:18009305..18012045,5	K562	blood:
2	chr17:17989884..17994353-chr17:18008301..18011863,4	MCF-7	breast:
3	chr17:18007007..18008585-chr17:18011589..18013521,2	MCF-7	breast:
4	chr17:18006973..18009716-chr17:18011197..18014211,3	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATPAF2-2	chr17:18011670-18011949	NONHSAT146146
2	lnc-ATPAF2-2	chr17:18011670-18011949	NONHSAT146143
3	lnc-ATPAF2-2	chr17:18011670-18011949	NONHSAT146144
4	lnc-ATPAF2-2	chr17:18009717-18011949	NONHSAT146145
5	lnc-ATPAF2-2	chr17:18010648-18013777	NONHSAT146149
6	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: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11652894	0.87[ASN][1000 genomes]
rs12943202	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943914	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948749	0.87[ASN][1000 genomes]
rs12952818	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230316	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955351	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955360	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955371	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2955382	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4244602	0.82[JPT][hapmap]
rs4341796	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs4925138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002487	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs6502625	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs6502629	0.87[CEU][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]
rs712265	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207395	0.82[JPT][hapmap]
rs7222480	0.84[MEX][hapmap]
rs7224815	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs72827413	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080823	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs854762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854810	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs854764	TOM1L2	cis	cerebellum	SCAN
rs854764	DRG2	cis	Thyroid	GTEx
rs854764	SREBF1	cis	Whole Blood	GTEx
rs854764	C17orf39	cis	cerebellum	SCAN
rs854764	TOM1L2	cis	parietal	SCAN

Chromatin state (count:111 , 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	chr17:17994200-18011800	Strong transcription	Stomach Smooth Muscle	stomach
4	chr17:17994200-18012000	Strong transcription	Fetal Intestine Small	intestine
5	chr17:17994600-18012800	Strong transcription	Thymus	Thymus
6	chr17:18002400-18019600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr17:18003000-18011800	Weak transcription	NHDF-Ad	bronchial
8	chr17:18003200-18021000	Weak transcription	Psoas Muscle	Psoas
9	chr17:18003400-18012400	Weak transcription	Hela-S3	cervix
10	chr17:18003800-18015200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:18004000-18012200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:18004200-18011800	Weak transcription	GM12878-XiMat	blood
13	chr17:18004800-18015400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr17:18005400-18012800	Weak transcription	Osteobl	bone
15	chr17:18005400-18013600	Weak transcription	HSMM	muscle
16	chr17:18005400-18017000	Weak transcription	HepG2	liver
17	chr17:18005600-18012200	Weak transcription	NH-A	brain
18	chr17:18005600-18015000	Weak transcription	HMEC	breast
19	chr17:18005800-18014800	Weak transcription	HSMMtube	muscle
20	chr17:18006400-18011800	Strong transcription	Spleen	Spleen
21	chr17:18006800-18012800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr17:18007200-18011800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr17:18007800-18012400	Weak transcription	Left Ventricle	heart
24	chr17:18008400-18012400	Weak transcription	Fetal Lung	lung
25	chr17:18009000-18015000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:18009600-18012400	Weak transcription	Colon Smooth Muscle	Colon
27	chr17:18010000-18012200	Weak transcription	Brain Substantia Nigra	brain
28	chr17:18010200-18013000	Enhancers	Fetal Brain Male	brain
29	chr17:18010200-18014200	Genic enhancers	Liver	Liver
30	chr17:18010200-18015000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr17:18010400-18012000	Weak transcription	Primary B cells from cord blood	blood
32	chr17:18010400-18012000	Weak transcription	Brain Angular Gyrus	brain
33	chr17:18010400-18012200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:18010400-18013000	Weak transcription	NHEK	skin
35	chr17:18010600-18012200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr17:18010600-18015400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr17:18010600-18015800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr17:18010600-18030400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr17:18010800-18011800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr17:18010800-18012400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr17:18010800-18012400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr17:18010800-18012400	Weak transcription	Aorta	Aorta
43	chr17:18010800-18012600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr17:18010800-18012600	Weak transcription	Dnd41	blood
45	chr17:18010800-18013000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr17:18010800-18013000	Weak transcription	Pancreas	Pancrea
47	chr17:18010800-18014000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:18010800-18015400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr17:18010800-18020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr17:18011000-18012600	Weak transcription	Primary T cells from cord blood	blood

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