Variant report

Variant	rs10415521
Chromosome Location	chr19:56188772-56188773
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	FOS	chr19:56188477-56188811	MCF10A-Er-Src	breast:	n/a	chr19:56188755-56188764
2	EBF1	chr19:56188355-56188909	GM12878	blood:	n/a	chr19:56188470-56188481
3	POLR2A	chr19:56188478-56190026	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:56188228-56190484	GM18505	blood:	n/a	n/a
5	WRNIP1	chr19:56187896-56190180	GM12878	blood:	n/a	n/a
6	EP300	chr19:56188770-56189124	K562	blood:	n/a	n/a
7	JUND	chr19:56188588-56189003	K562	blood:	n/a	chr19:56188755-56188764
8	MTA3	chr19:56188510-56190298	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:56188204-56190273	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:56188358-56190377	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:56188756-56189433	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
2	chr19:56185642..56190165-chr19:56193908..56196750,4	MCF-7	breast:
3	chr19:56187596..56189855-chr19:56218072..56219589,2	K562	blood:
4	chr19:56188121..56189803-chr19:56212346..56215225,2	K562	blood:
5	chr19:56188015..56189897-chr19:56203911..56206682,2	MCF-7	breast:
6	chr19:55918601..55920426-chr19:56186578..56189029,2	K562	blood:
7	chr19:56172318..56174905-chr19:56187838..56190897,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267523	TF binding region
EPN1	TF binding region
ENSG00000211571	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000268593	Chromatin interaction
ENSG00000267117	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000063245	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10402618	0.89[ASN][1000 genomes]
rs10403866	0.95[ASN][1000 genomes]
rs10408613	0.91[ASN][1000 genomes]
rs10410404	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.80[MKK][hapmap];0.87[ASN][1000 genomes]
rs10410802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410886	0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10412050	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10417539	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10421319	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs11882031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287791	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs28385383	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28595590	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668166	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs310437	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs310441	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745446	0.81[ASN][1000 genomes]
rs4801526	0.81[ASN][1000 genomes]
rs523509	0.85[ASN][1000 genomes]
rs575274	0.88[JPT][hapmap]
rs57544196	0.96[ASN][1000 genomes]
rs584405	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60873246	0.92[ASN][1000 genomes]
rs610811	0.81[JPT][hapmap]
rs617073	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648651	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs681804	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7256441	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73613281	0.95[ASN][1000 genomes]
rs8100143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109983	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv522559	chr19:56185250-56190815	Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56187000-56189600	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr19:56187000-56189600	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr19:56187200-56189600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:56187200-56189800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
5	chr19:56187200-56190000	Flanking Active TSS	Liver	Liver
6	chr19:56187200-56190000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr19:56187400-56189400	Transcr. at gene 5' and 3'	K562	blood
8	chr19:56187600-56188800	Flanking Active TSS	HepG2	liver
9	chr19:56187600-56189000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:56187600-56189000	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr19:56187600-56189200	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr19:56187600-56189200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr19:56187600-56189400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:56187600-56189400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr19:56187600-56189400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:56187600-56189600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:56187600-56189800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:56187600-56190200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:56187600-56190600	Genic enhancers	Fetal Muscle Leg	muscle
20	chr19:56187600-56190800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:56187800-56189200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:56187800-56189200	Flanking Active TSS	Fetal Intestine Large	intestine
23	chr19:56187800-56189400	Enhancers	Brain Substantia Nigra	brain
24	chr19:56187800-56189400	Enhancers	Psoas Muscle	Psoas
25	chr19:56187800-56189800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:56187800-56189800	Enhancers	Ovary	ovary
27	chr19:56187800-56190200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:56187800-56192400	Genic enhancers	Placenta	Placenta
29	chr19:56188000-56188800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr19:56188000-56188800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:56188000-56188800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:56188000-56188800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr19:56188000-56188800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr19:56188000-56188800	Enhancers	NH-A	brain
35	chr19:56188000-56189000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr19:56188000-56189000	Genic enhancers	Fetal Stomach	stomach
37	chr19:56188000-56189000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr19:56188000-56189000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr19:56188000-56189200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:56188000-56189200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:56188000-56189200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr19:56188000-56189200	Enhancers	Right Ventricle	heart
43	chr19:56188000-56189200	Enhancers	NHDF-Ad	bronchial
44	chr19:56188000-56189200	Transcr. at gene 5' and 3'	NHEK	skin
45	chr19:56188000-56189400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr19:56188000-56189400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:56188000-56189400	Weak transcription	Aorta	Aorta
48	chr19:56188000-56189600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr19:56188000-56189600	Genic enhancers	Brain Angular Gyrus	brain
50	chr19:56188000-56189600	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links