Variant report

Variant	rs17387413
Chromosome Location	chr1:45112442-45112443
allele	C/T
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	POLR2A	chr1:45112269-45112960	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:45112383-45112690	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:45112316-45112517	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr1:45110860-45113081	IMR90	lung:	n/a	n/a
5	POLR2A	chr1:45112124-45112906	K562	blood:	n/a	n/a
6	POLR2A	chr1:45112289-45112964	K562	blood:	n/a	n/a
7	POLR2A	chr1:45112231-45113098	GM12878	blood:	n/a	n/a
8	MAZ	chr1:45110967-45112811	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45112025..45113914-chr1:45115566..45117963,2	MCF-7	breast:
2	chr1:45090489..45092386-chr1:45110257..45112977,2	MCF-7	breast:
3	chr1:45096002..45100159-chr1:45110119..45116077,6	MCF-7	breast:

Variant related genes	Relation type
RNF220	TF binding region
ENSG00000187147	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1051648	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1051664	0.81[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs11581172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11582970	0.89[EUR][1000 genomes]
rs12731688	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1407144	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2018706	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2281759	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2355365	0.90[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs2822	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34296911	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3444	0.95[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs35791258	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3768439	0.95[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs3850852	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41269061	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4660283	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4660284	0.95[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs4660285	0.94[EUR][1000 genomes]
rs4660815	0.95[CEU][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4660816	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4660817	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57291201	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72671954	0.94[EUR][1000 genomes]
rs74070566	0.90[EUR][1000 genomes]
rs876511	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs876512	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs995089	0.90[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	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
7	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45098400-45116000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45099000-45115600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:45099000-45116800	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr1:45099000-45117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:45099000-45117800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:45099200-45117600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:45099200-45118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:45099400-45115000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:45099400-45115600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:45099400-45117200	Strong transcription	Placenta	Placenta
11	chr1:45099400-45120800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:45099400-45121000	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:45099400-45121200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:45099600-45114600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:45099600-45115400	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:45099600-45115600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:45099600-45117200	Strong transcription	Primary B cells from cord blood	blood
18	chr1:45099600-45117200	Strong transcription	Primary hematopoietic stem cells	blood
19	chr1:45099600-45118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:45099600-45118800	Strong transcription	Fetal Thymus	thymus
21	chr1:45099800-45115400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:45099800-45117400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:45099800-45118200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:45099800-45118400	Strong transcription	Thymus	Thymus
25	chr1:45099800-45121200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:45099800-45121600	Strong transcription	Brain Germinal Matrix	brain
27	chr1:45099800-45125600	Strong transcription	Lung	lung
28	chr1:45100000-45113600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:45100000-45113600	Strong transcription	Hela-S3	cervix
30	chr1:45100000-45117400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:45100000-45118600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:45100200-45117400	Strong transcription	HepG2	liver
33	chr1:45100200-45118000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:45100200-45119800	Strong transcription	Primary T cells from cord blood	blood
35	chr1:45100400-45114600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:45100400-45117200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:45100400-45117400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr1:45100400-45118400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:45100400-45120800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:45100600-45117200	Strong transcription	Dnd41	blood
41	chr1:45100600-45118400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:45100800-45113600	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr1:45100800-45115400	Strong transcription	GM12878-XiMat	blood
44	chr1:45100800-45117400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:45101000-45118800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:45101200-45118400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:45101600-45116800	Genic enhancers	Fetal Muscle Leg	muscle
48	chr1:45102600-45117400	Strong transcription	Left Ventricle	heart
49	chr1:45103600-45121400	Strong transcription	Fetal Brain Female	brain
50	chr1:45104000-45138200	Weak transcription	Fetal Brain Male	brain

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