Variant report

Variant	rs717225
Chromosome Location	chr19:42393286-42393287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:42393166-42393292	MCF-7	breast:	n/a	n/a
2	CTCF	chr19:42393185-42393295	MCF-7	breast:	n/a	n/a
3	WRNIP1	chr19:42393276-42393309	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:42392970-42393988	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:42389937-42394570	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:42393206-42393562	GM12878	blood:	n/a	n/a
7	CTCF	chr19:42393160-42393310	A549	lung:	n/a	n/a
8	POLR2A	chr19:42392694-42394464	HL-60	blood:	n/a	n/a
9	POLR2A	chr19:42392928-42393537	GM12892	blood:	n/a	n/a
10	CTCF	chr19:42393185-42393309	GM12891	blood:	n/a	n/a
11	CTCF	chr19:42393158-42393318	HepG2	liver:	n/a	n/a
12	CTCF	chr19:42393193-42393325	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr19:42393205-42393289	MCF-7	breast:	n/a	n/a
14	CTCF	chr19:42393160-42393310	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:42389706-42394346	SK-N-MC	brain:	n/a	n/a
16	CTCF	chr19:42393199-42393303	MCF-7	breast:	n/a	n/a
17	CTCF	chr19:42393160-42393310	HEK293	kidney:	n/a	n/a
18	POLR2A	chr19:42393066-42393414	K562	blood:	n/a	n/a
19	CTCF	chr19:42393240-42393390	GM12873	blood:	n/a	n/a
20	POLR2A	chr19:42393181-42394299	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42390528..42393391-chr19:42425919..42428755,3	MCF-7	breast:
2	chr19:42392091..42393958-chr19:42398936..42401032,2	MCF-7	breast:
3	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:
4	chr19:42390140..42393678-chr19:42394261..42398306,6	K562	blood:
5	chr19:42387920..42390020-chr19:42392761..42394560,2	K562	blood:
6	chr19:42392649..42394240-chr19:42444125..42445799,2	K562	blood:
7	chr19:42392649..42394597-chr19:42444299..42446672,2	K562	blood:
8	chr19:42390499..42394130-chr19:42395488..42398499,5	MCF-7	breast:
9	chr19:42392209..42393764-chr19:42436323..42438762,2	MCF-7	breast:
10	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
11	chr19:42385266..42389164-chr19:42392215..42397025,5	MCF-7	breast:
12	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:
13	chr19:42392300..42393961-chr19:42403075..42405096,2	K562	blood:

No data

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000076928	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10401189	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10401937	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10402667	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10403081	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10414811	1.00[CEU][hapmap]
rs10417495	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10419314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083638	1.00[CEU][hapmap]
rs11083640	1.00[CEU][hapmap]
rs11878536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11878555	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs11878734	1.00[CEU][hapmap]
rs11879437	1.00[CEU][hapmap]
rs11880977	1.00[CEU][hapmap]
rs11881323	1.00[CEU][hapmap]
rs11883018	1.00[CEU][hapmap]
rs12104228	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16975619	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2288510	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2288511	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2288512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2303798	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28396197	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28521795	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28706300	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3745222	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6509003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7252790	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7252800	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7253691	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7260129	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs73550603	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73550610	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73550618	1.00[EUR][1000 genomes]
rs8109784	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8109959	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8110305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8113339	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8113686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs891169	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs891170	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs891171	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs891172	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9653098	1.00[CEU][hapmap]
rs9989667	1.00[CEU][hapmap]

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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389000-42396000	Weak transcription	Aorta	Aorta
2	chr19:42389000-42396000	Weak transcription	Ovary	ovary
3	chr19:42389200-42407200	Weak transcription	Fetal Kidney	kidney
4	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
5	chr19:42389400-42393600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:42389400-42398200	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:42389400-42402000	Weak transcription	Psoas Muscle	Psoas
8	chr19:42389400-42406000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:42389400-42411400	Weak transcription	Fetal Brain Male	brain
10	chr19:42389800-42409000	Strong transcription	Fetal Stomach	stomach
11	chr19:42390800-42411200	Weak transcription	Hela-S3	cervix
12	chr19:42391000-42394000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
13	chr19:42391200-42393800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:42391400-42396800	Weak transcription	Brain Anterior Caudate	brain
15	chr19:42391400-42407400	Weak transcription	K562	blood
16	chr19:42391600-42393400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:42391600-42396000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:42391600-42399600	Weak transcription	HUVEC	blood vessel
19	chr19:42391600-42404600	Weak transcription	HSMM	muscle
20	chr19:42392000-42394000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
21	chr19:42392000-42394400	Strong transcription	Esophagus	oesophagus
22	chr19:42392000-42394400	Strong transcription	NHLF	lung
23	chr19:42392000-42399600	Strong transcription	Lung	lung
24	chr19:42392000-42404000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:42392000-42412600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:42392000-42412600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:42392000-42412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:42392200-42393400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
29	chr19:42392200-42393600	Strong transcription	Fetal Brain Female	brain
30	chr19:42392200-42394000	Strong transcription	Brain Germinal Matrix	brain
31	chr19:42392200-42395600	Weak transcription	Right Ventricle	heart
32	chr19:42392200-42397400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr19:42392200-42400800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:42392200-42401400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:42392200-42407600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:42392200-42408400	Strong transcription	Liver	Liver
37	chr19:42392200-42412400	Strong transcription	Fetal Muscle Leg	muscle
38	chr19:42392200-42412800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr19:42392400-42393400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
40	chr19:42392400-42393800	Enhancers	Primary hematopoietic stem cells	blood
41	chr19:42392400-42394200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:42392400-42394200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:42392400-42394200	Genic enhancers	Dnd41	blood
44	chr19:42392400-42396000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr19:42392400-42398200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr19:42392400-42399200	Weak transcription	Fetal Lung	lung
47	chr19:42392400-42399600	Weak transcription	Small Intestine	intestine
48	chr19:42392400-42399800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr19:42392400-42400400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr19:42392400-42401800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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