Variant report

Variant	rs10465818
Chromosome Location	chr1:45244692-45244693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:70)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:70 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45243922-45247518	U87	brain:	n/a	n/a
2	POLR2A	chr1:45243842-45247542	A549	lung:	n/a	n/a
3	POLR2A	chr1:45240631-45247540	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45240526-45248028	GM12892	blood:	n/a	n/a
5	EBF1	chr1:45244421-45244751	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:45244381-45244707	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:45244418-45244747	ECC-1	luminal epithelium:	n/a	n/a
8	HEY1	chr1:45243695-45244848	K562	blood:	n/a	n/a
9	PML	chr1:45244288-45245048	K562	blood:	n/a	n/a
10	POLR2A	chr1:45240483-45248016	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:45244430-45244701	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:45240295-45248263	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:45242580-45247462	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:45240547-45249219	HepG2	liver:	n/a	n/a
15	NR2F2	chr1:45244447-45244942	K562	blood:	n/a	n/a
16	HEY1	chr1:45244410-45245079	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:45239529-45250168	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr1:45244506-45244845	GM12891	blood:	n/a	n/a
19	TEAD4	chr1:45244453-45244872	K562	blood:	n/a	n/a
20	POLR2A	chr1:45244438-45244913	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:45242766-45248217	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:45243808-45245472	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:45242928-45247383	H1-hESC	embryonic stem cell:	n/a	n/a
24	NFATC1	chr1:45244417-45244863	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:45240546-45248272	GM12892	blood:	n/a	n/a
26	POLR2A	chr1:45243686-45245094	K562	blood:	n/a	n/a
27	POLR2A	chr1:45243851-45245038	K562	blood:	n/a	n/a
28	HEY1	chr1:45243835-45245001	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:45242629-45247224	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr1:45243708-45245616	K562	blood:	n/a	n/a
31	POLR2A	chr1:45242979-45245039	K562	blood:	n/a	n/a
32	POLR2A	chr1:45240508-45247317	GM12878	blood:	n/a	n/a
33	ATF2	chr1:45244454-45244967	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr1:45240713-45247745	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr1:45243001-45245051	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:45243853-45247621	U87	brain:	n/a	n/a
37	POLR2A	chr1:45244337-45244903	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:45240271-45247480	K562	blood:	n/a	n/a
39	POLR2A	chr1:45244447-45244966	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr1:45243714-45245109	HL-60	blood:	n/a	n/a
41	POLR2A	chr1:45239953-45247379	K562	blood:	n/a	n/a
42	POLR2A	chr1:45243824-45245068	K562	blood:	n/a	n/a
43	POLR2A	chr1:45244432-45244731	U87	brain:	n/a	n/a
44	POLR2A	chr1:45240502-45248124	GM12878	blood:	n/a	n/a
45	MTA3	chr1:45244377-45244869	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:45244538-45244881	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr1:45244429-45244718	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr1:45243011-45245009	K562	blood:	n/a	n/a
49	POLR2A	chr1:45244620-45245035	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr1:45240324-45245069	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
2	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
3	chr1:45239101..45240995-chr1:45242933..45244701,2	MCF-7	breast:
4	chr1:45239959..45246724-chr1:45282430..45287057,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225721	TF binding region
ENSG00000126107	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10127448	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211030	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211031	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211034	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11211037	0.84[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap]
rs11211046	0.87[ASW][hapmap];0.94[GIH][hapmap]
rs11584031	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11801067	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11808189	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11808852	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12059964	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[YRI][hapmap]
rs12094028	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12117881	0.86[ASN][1000 genomes]
rs12136048	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12136099	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12410588	0.82[ASN][1000 genomes]
rs12742914	0.87[ASN][1000 genomes]
rs16832228	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273940	0.81[ASN][1000 genomes]
rs263966	0.81[GIH][hapmap]
rs263975	0.81[ASW][hapmap];0.91[GIH][hapmap]
rs263986	0.81[JPT][hapmap]
rs3795720	0.94[GIH][hapmap]
rs4542248	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6429548	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6656337	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6658470	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6666987	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671255	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6678729	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685176	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6688710	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698847	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7512710	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514741	0.81[ASN][1000 genomes]
rs7518836	0.91[ASN][1000 genomes]
rs7524446	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs7525308	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs7536146	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7545808	0.81[ASN][1000 genomes]
rs7550170	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554177	0.86[GIH][hapmap]
rs7555065	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9645347	0.81[ASN][1000 genomes]
rs9988451	0.87[ASW][hapmap]
rs9988580	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
11	nsv947252	chr1:45242176-45258816	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
12	nsv945912	chr1:45243841-45248516	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10465818	SNORD38B	cis	cerebellum	SCAN
rs10465818	EIF2B3	cis	cerebellum	SCAN
rs10465818	C1orf84	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45241600-45244800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:45241800-45244800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:45241800-45244800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:45241800-45244800	Transcr. at gene 5' and 3'	A549	lung
5	chr1:45241800-45244800	Transcr. at gene 5' and 3'	K562	blood
6	chr1:45241800-45245000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
7	chr1:45242000-45245000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:45242000-45245000	Transcr. at gene 5' and 3'	Hela-S3	cervix
9	chr1:45242200-45244800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
10	chr1:45242400-45244800	Genic enhancers	Stomach Mucosa	stomach
11	chr1:45242400-45246400	Strong transcription	Aorta	Aorta
12	chr1:45242600-45247600	Strong transcription	Brain Hippocampus Middle	brain
13	chr1:45242800-45244800	Genic enhancers	NHDF-Ad	bronchial
14	chr1:45242800-45247400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:45242800-45247800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:45243000-45244800	Genic enhancers	Brain Cingulate Gyrus	brain
17	chr1:45243000-45244800	Strong transcription	Fetal Kidney	kidney
18	chr1:45243000-45244800	Genic enhancers	Fetal Thymus	thymus
19	chr1:45243000-45245400	Strong transcription	Rectal Smooth Muscle	rectum
20	chr1:45243000-45245600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:45243000-45246600	Strong transcription	Brain Anterior Caudate	brain
22	chr1:45243000-45247200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:45243200-45244800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:45243200-45244800	Strong transcription	Ovary	ovary
25	chr1:45243200-45246200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:45243200-45246400	Strong transcription	HSMMtube	muscle
27	chr1:45243200-45247000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:45243200-45247400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:45243400-45244800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:45243400-45245000	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr1:45243400-45245000	Strong transcription	Brain Substantia Nigra	brain
32	chr1:45243400-45245000	Strong transcription	Colon Smooth Muscle	Colon
33	chr1:45243400-45246800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:45243400-45247200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr1:45243400-45247400	Strong transcription	Liver	Liver
36	chr1:45243400-45248200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:45243400-45249000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:45243600-45244800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:45243600-45244800	Strong transcription	Brain Angular Gyrus	brain
40	chr1:45243600-45244800	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr1:45243600-45244800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr1:45243600-45245000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:45243600-45245000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:45243600-45245000	Genic enhancers	Osteobl	bone
45	chr1:45243600-45245200	Strong transcription	Gastric	stomach
46	chr1:45243600-45245600	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr1:45243600-45245800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:45243600-45246600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:45243600-45246800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:45243600-45247200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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