Variant report

Variant	rs10417495
Chromosome Location	chr19:42416241-42416242
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:42415836-42416800	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:42415780-42416673	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:42416089-42416248	A549	lung:	n/a	n/a
4	POLR2A	chr19:42416024-42416429	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr19:42413672-42416851	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:42414321-42416435	GM12891	blood:	n/a	n/a
7	SUZ12	chr19:42415904-42416789	H1-hESC	embryonic stem cell:	n/a	n/a
8	SUZ12	chr19:42416055-42418681	NT2-D1	testis:	n/a	n/a
9	POLR2A	chr19:42416114-42416625	H1-hESC	embryonic stem cell:	n/a	n/a
10	BCL3	chr19:42415731-42416728	A549	lung:	n/a	chr19:42416437-42416446
11	POLR2A	chr19:42414460-42416713	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:42413748-42416743	GM12891	blood:	n/a	n/a
13	NFATC1	chr19:42415795-42416595	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:42416154-42416595	GM12878	blood:	n/a	n/a
15	NFATC1	chr19:42414842-42416294	GM12878	blood:	n/a	n/a
16	STAT5A	chr19:42415968-42416470	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:42412043-42416925	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:42416045-42416316	ECC-1	luminal epithelium:	n/a	n/a
19	PAX5	chr19:42415990-42416267	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:42412744-42416335	GM18505	blood:	n/a	n/a
21	MTA3	chr19:42415724-42416721	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:42415808-42416472	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr19:42416140-42416642	HepG2	liver:	n/a	n/a
24	POLR2A	chr19:42416048-42416568	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr19:42415798-42416790	GM12878	blood:	n/a	n/a
26	BCL3	chr19:42415922-42416651	A549	lung:	n/a	chr19:42416437-42416446
27	POLR2A	chr19:42412083-42416861	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:42415868-42416477	Hela-S3	cervix:	n/a	n/a
29	RUNX3	chr19:42415940-42416389	GM12878	blood:	n/a	n/a
30	PAX5	chr19:42416009-42416321	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:42414066-42416690	U87	brain:	n/a	n/a
32	POLR2A	chr19:42415841-42416605	GM12878	blood:	n/a	n/a
33	BCLAF1	chr19:42416115-42416467	GM12878	blood:	n/a	chr19:42416437-42416446
34	POLR2A	chr19:42414065-42416690	U87	brain:	n/a	n/a
35	POLR2A	chr19:42415828-42416626	HCT-116	colon:	n/a	n/a
36	POLR2A	chr19:42415815-42416411	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr19:42416228-42416633	K562	blood:	n/a	n/a
38	POLR2A	chr19:42413247-42416753	GM12892	blood:	n/a	n/a
39	RUNX3	chr19:42415986-42416360	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:42414263-42416523	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr19:42412700-42416805	GM12878	blood:	n/a	n/a
42	PML	chr19:42415932-42416457	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:42416010-42416740	MCF-7	breast:	n/a	n/a
44	POLR2A	chr19:42412681-42416659	A549	lung:	n/a	n/a
45	POLR2A	chr19:42412140-42416485	K562	blood:	n/a	n/a
46	POLR2A	chr19:42412121-42416922	GM12892	blood:	n/a	n/a
47	POLR2A	chr19:42415660-42416860	GM12891	blood:	n/a	n/a
48	PAX5	chr19:42416041-42416326	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:42412075-42416779	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr19:42416138-42416584	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:42406489..42409925-chr19:42413611..42416710,4	K562	blood:
2	chr19:42414489..42417450-chr19:42430413..42434509,3	K562	blood:
3	chr19:42408822..42410567-chr19:42416215..42418825,2	MCF-7	breast:
4	chr19:42408977..42410880-chr19:42415090..42416805,2	MCF-7	breast:
5	chr19:42386109..42390387-chr19:42411996..42416642,6	K562	blood:
6	chr19:42400409..42404033-chr19:42410840..42416491,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268041	TF binding region
ENSG00000076928	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10401189	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10401937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10402667	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10403081	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11083638	1.00[CEU][hapmap]
rs11083640	1.00[CEU][hapmap]
rs11878536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11878555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs11878734	1.00[CEU][hapmap]
rs11878811	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	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16975619	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2288509	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];0.88[ASN][1000 genomes]
rs2288510	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2288511	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2288512	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303798	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];0.98[ASN][1000 genomes]
rs28396197	0.93[AMR][1000 genomes]
rs28521795	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28706300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3745222	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6509003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs717225	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]
rs7252790	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7252800	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7253691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7260129	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs73550603	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73550610	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550618	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109784	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8109959	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8110305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8113339	1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8113686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs891169	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs891170	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs891171	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs891172	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9653098	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
2	chr19:42412600-42416600	Weak transcription	Gastric	stomach
3	chr19:42412600-42419600	Weak transcription	Ovary	ovary
4	chr19:42414200-42416400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr19:42414400-42417800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr19:42414800-42416800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:42414800-42417200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr19:42414800-42418000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr19:42415200-42417000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr19:42415200-42417600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr19:42415200-42418400	Weak transcription	Dnd41	blood
12	chr19:42415400-42416400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:42415400-42419800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr19:42415600-42419400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr19:42415800-42416600	Enhancers	Spleen	Spleen
16	chr19:42415800-42417800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:42415800-42419000	Enhancers	Primary B cells from cord blood	blood
18	chr19:42416000-42416400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:42416000-42416400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:42416000-42416600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:42416000-42416600	Bivalent Enhancer	Primary T cells from cord blood	blood
22	chr19:42416000-42418000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:42416000-42418200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:42416000-42418600	Bivalent Enhancer	Fetal Thymus	thymus
25	chr19:42416200-42416400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
26	chr19:42416200-42416400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:42416200-42416400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
28	chr19:42416200-42416400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
29	chr19:42416200-42416400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:42416200-42416400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:42416200-42416400	Bivalent Enhancer	Fetal Kidney	kidney
32	chr19:42416200-42416400	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr19:42416200-42416400	Enhancers	Pancreas	Pancrea
34	chr19:42416200-42416600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr19:42416200-42416600	Bivalent Enhancer	GM12878-XiMat	blood
36	chr19:42416200-42416800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:42416200-42416800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:42416200-42416800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:42416200-42417000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:42416200-42417200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:42416200-42417400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:42416200-42417600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
43	chr19:42416200-42418200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr19:42416200-42419400	Bivalent Enhancer	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links