Variant report

Variant	rs1418718
Chromosome Location	chr1:192776414-192776415
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	FOS	chr1:192776343-192777370	MCF10A-Er-Src	breast:	n/a	chr1:192777174-192777181 chr1:192776620-192776630 chr1:192777172-192777183 chr1:192776622-192776629 chr1:192777173-192777182 chr1:192777174-192777182 chr1:192776621-192776629
2	CREB1	chr1:192776362-192776905	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:192776209-192783463	IMR90	lung:	n/a	n/a
4	MAX	chr1:192776343-192778901	A549	lung:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
5	EP300	chr1:192776405-192776691	GM12878	blood:	n/a	n/a
6	POU2F2	chr1:192776128-192776915	GM12878	blood:	n/a	chr1:192776231-192776241 chr1:192776656-192776669 chr1:192776228-192776242 chr1:192776658-192776668 chr1:192776228-192776243 chr1:192776658-192776668 chr1:192776229-192776240 chr1:192776232-192776239 chr1:192776225-192776238 chr1:192776231-192776240 chr1:192776657-192776669 chr1:192776229-192776242 chr1:192776866-192776881 chr1:192776230-192776242 chr1:192776658-192776667 chr1:192776135-192776148 chr1:192776231-192776241 chr1:192776226-192776244 chr1:192776868-192776883 chr1:192776231-192776239 chr1:192776230-192776240 chr1:192776224-192776245
7	POLR2A	chr1:192775823-192784756	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr1:192776231-192777354	MCF10A-Er-Src	breast:	n/a	chr1:192777173-192777182 chr1:192776876-192776883 chr1:192777174-192777183
9	STAT3	chr1:192776345-192777421	MCF10A-Er-Src	breast:	n/a	chr1:192777173-192777182 chr1:192776876-192776883 chr1:192777174-192777183
10	STAT3	chr1:192776358-192776879	GM12878	blood:	n/a	n/a
11	FOS	chr1:192776360-192777630	HUVEC	blood vessel:	n/a	chr1:192777174-192777181 chr1:192776620-192776630 chr1:192777172-192777183 chr1:192776622-192776629 chr1:192777173-192777182 chr1:192777174-192777182 chr1:192776621-192776629
12	FOSL2	chr1:192776395-192777453	A549	lung:	n/a	chr1:192777174-192777181 chr1:192776620-192776630 chr1:192776622-192776629 chr1:192777173-192777182 chr1:192777174-192777182 chr1:192776621-192776629
13	CHD1	chr1:192776053-192782472	IMR90	lung:	n/a	n/a
14	POLR2A	chr1:192775981-192784209	MCF10A-Er-Src	breast:	n/a	n/a
15	EP300	chr1:192776309-192776770	GM12878	blood:	n/a	n/a
16	STAT3	chr1:192776249-192777423	MCF10A-Er-Src	breast:	n/a	chr1:192777173-192777182 chr1:192776876-192776883 chr1:192777174-192777183
17	MXI1	chr1:192776009-192779800	IMR90	lung:	n/a	chr1:192777343-192777352
18	FOS	chr1:192776194-192777467	MCF10A-Er-Src	breast:	n/a	chr1:192777174-192777181 chr1:192776620-192776630 chr1:192777172-192777183 chr1:192776622-192776629 chr1:192777173-192777182 chr1:192777174-192777182 chr1:192776621-192776629
19	TBL1XR1	chr1:192776359-192776701	GM12878	blood:	n/a	n/a
20	FOS	chr1:192776407-192777428	MCF10A-Er-Src	breast:	n/a	chr1:192777174-192777181 chr1:192776620-192776630 chr1:192777172-192777183 chr1:192776622-192776629 chr1:192777173-192777182 chr1:192777174-192777182 chr1:192776621-192776629
21	EP300	chr1:192776375-192776776	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:192775702..192778041-chr1:192986871..192988604,2	MCF-7	breast:
2	chr1:192768183..192771831-chr1:192775042..192777243,3	K562	blood:
3	chr1:192775703..192778053-chr1:193028205..193029898,2	MCF-7	breast:
4	chr1:192773238..192775392-chr1:192775635..192777815,2	K562	blood:
5	chr1:192459062..192461935-chr1:192775675..192778515,2	K562	blood:
6	chr1:192774228..192777200-chr1:192803483..192805431,2	MCF-7	breast:
7	chr1:192774987..192776669-chr1:192777347..192780791,3	K562	blood:
8	chr1:192775766..192777613-chr1:192802344..192805276,2	K562	blood:
9	chr1:192775115..192776767-chr1:192778310..192780018,2	K562	blood:

Variant related genes	Relation type
RGS2	TF binding region
ENSG00000116747	Chromatin interaction
ENSG00000116741	Chromatin interaction
ENSG00000116750	Chromatin interaction
ENSG00000221145	Chromatin interaction
ENSG00000226814	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10801151	0.91[CEU][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes]
rs10801152	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10801153	0.91[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs10801154	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs10801155	0.84[ASN][1000 genomes]
rs10801156	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10801157	0.84[EUR][1000 genomes]
rs10801158	0.84[EUR][1000 genomes]
rs10921267	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs10921268	0.90[EUR][1000 genomes]
rs11586572	0.96[EUR][1000 genomes]
rs12565835	0.97[EUR][1000 genomes]
rs16834851	0.95[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs1819741	0.91[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1890398	0.83[ASN][1000 genomes]
rs1890399	0.84[ASN][1000 genomes]
rs1933694	0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs2746071	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746072	0.92[EUR][1000 genomes]
rs2746073	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs6428136	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6669632	0.91[EUR][1000 genomes]
rs6684156	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703040	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs7525778	0.96[EUR][1000 genomes]
rs7534336	0.90[ASN][1000 genomes]
rs7546861	0.96[EUR][1000 genomes]
rs7549721	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv548660	chr1:192609268-192945348	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192766200-192777200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:192775200-192776600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:192775200-192776800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr1:192775200-192777200	Enhancers	Hela-S3	cervix
5	chr1:192775400-192776600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:192775400-192777600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr1:192775400-192777800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr1:192775800-192776600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:192775800-192777000	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr1:192775800-192777200	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr1:192775800-192777200	Flanking Active TSS	GM12878-XiMat	blood
12	chr1:192775800-192777400	Enhancers	Small Intestine	intestine
13	chr1:192775800-192777400	Active TSS	Stomach Smooth Muscle	stomach
14	chr1:192775800-192777600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:192775800-192777800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr1:192775800-192778200	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:192776000-192777000	Active TSS	A549	lung
18	chr1:192776000-192777400	Enhancers	HSMM	muscle
19	chr1:192776000-192777600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:192776000-192777800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr1:192776000-192777800	Flanking Active TSS	HUVEC	blood vessel
22	chr1:192776000-192778800	Active TSS	Colon Smooth Muscle	Colon
23	chr1:192776200-192776600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
24	chr1:192776200-192776600	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr1:192776200-192776600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr1:192776200-192776600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:192776200-192776600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:192776200-192776600	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr1:192776200-192776600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:192776200-192776600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr1:192776200-192776800	Active TSS	Brain Substantia Nigra	brain
32	chr1:192776200-192776800	Flanking Active TSS	NHLF	lung
33	chr1:192776200-192777000	Active TSS	Brain Angular Gyrus	brain
34	chr1:192776200-192777200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:192776200-192777200	Active TSS	Right Atrium	heart
36	chr1:192776200-192777600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:192776200-192777600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr1:192776200-192777600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:192776200-192777600	Flanking Active TSS	Fetal Lung	lung
40	chr1:192776200-192777600	Flanking Active TSS	NHEK	skin
41	chr1:192776200-192777800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr1:192776200-192777800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:192776200-192777800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr1:192776200-192780600	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr1:192776400-192776600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:192776400-192776600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:192776400-192776600	Enhancers	Psoas Muscle	Psoas
48	chr1:192776400-192776600	Enhancers	NH-A	brain
49	chr1:192776400-192776800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:192776400-192776800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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