Variant report

Variant	rs10410802
Chromosome Location	chr19:56201817-56201818
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	PAX5	chr19:56201598-56201966	GM12891	blood:	n/a	chr19:56201833-56201842 chr19:56201831-56201850 chr19:56201833-56201851 chr19:56201832-56201849
2	POLR2A	chr19:56201613-56201990	GM12892	blood:	n/a	n/a
3	PAX5	chr19:56201493-56202130	GM12878	blood:	n/a	chr19:56201833-56201842 chr19:56201831-56201850 chr19:56201833-56201851 chr19:56201522-56201531 chr19:56201832-56201849
4	PAX5	chr19:56201674-56201908	GM12878	blood:	n/a	chr19:56201833-56201842 chr19:56201831-56201850 chr19:56201833-56201851 chr19:56201832-56201849
5	POLR2A	chr19:56201771-56201848	MCF-7	breast:	n/a	n/a
6	POLR2A	chr19:56201413-56201940	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:56201582-56201914	GM12878	blood:	n/a	n/a
8	PAX5	chr19:56201618-56201989	GM12878	blood:	n/a	chr19:56201833-56201842 chr19:56201831-56201850 chr19:56201833-56201851 chr19:56201832-56201849
9	POLR2A	chr19:56201630-56201953	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:56201794-56201832	K562	blood:	n/a	n/a
11	POLR2A	chr19:56201492-56201855	GM12892	blood:	n/a	n/a
12	PAX5	chr19:56201657-56202036	GM12892	blood:	n/a	chr19:56201833-56201842 chr19:56201831-56201850 chr19:56201833-56201851 chr19:56201832-56201849
13	POLR2A	chr19:56201725-56201945	HepG2	liver:	n/a	n/a
14	PAX5	chr19:56201621-56202018	GM12878	blood:	n/a	chr19:56201833-56201842 chr19:56201831-56201850 chr19:56201833-56201851 chr19:56201832-56201849

No.	Distal block	Cell Line	Cell type
1	chr19:56194384..56198254-chr19:56198433..56202813,4	K562	blood:
2	chr19:56186595..56191110-chr19:56199379..56202438,6	MCF-7	breast:
3	chr19:56176017..56178095-chr19:56199906..56202183,2	K562	blood:
4	chr19:56194595..56204961-chr19:56206160..56210902,10	K562	blood:
5	chr19:56197697..56202109-chr19:56204304..56207442,3	MCF-7	breast:

Variant related genes	Relation type
EPN1	TF binding region
ENSG00000267018	Chromatin interaction
ENSG00000203305	Chromatin interaction
ENSG00000267183	Chromatin interaction
ENSG00000267117	Chromatin interaction
ENSG00000211571	Chromatin interaction
ENSG00000063245	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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];0.97[CHD][hapmap];0.94[JPT][hapmap];0.80[MKK][hapmap];0.87[ASN][1000 genomes]
rs10410886	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10412050	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10415521	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]
rs10417539	0.96[ASN][1000 genomes]
rs10421319	0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs11882031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287791	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs28385383	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28595590	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668166	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs310437	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs310441	0.93[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	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs584405	0.88[AMR][1000 genomes];0.95[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];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648651	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs681804	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7256441	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73613281	0.95[ASN][1000 genomes]
rs8100143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109983	0.98[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10410802	ZNF580	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56188400-56211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:56188600-56210000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
7	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
8	chr19:56189000-56210000	Strong transcription	Fetal Brain Female	brain
9	chr19:56189200-56209400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:56189200-56212600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:56189400-56209400	Strong transcription	Fetal Thymus	thymus
12	chr19:56189400-56209400	Strong transcription	Dnd41	blood
13	chr19:56189400-56212400	Strong transcription	Brain Germinal Matrix	brain
14	chr19:56189600-56204600	Strong transcription	Brain Anterior Caudate	brain
15	chr19:56189600-56209400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:56189600-56209800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:56189600-56213200	Strong transcription	Primary T cells from cord blood	blood
18	chr19:56190000-56212600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr19:56190200-56210200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:56190200-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:56191000-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:56191400-56204600	Weak transcription	NHDF-Ad	bronchial
23	chr19:56191800-56203000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr19:56191800-56218800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:56192000-56214600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr19:56192200-56209800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:56192200-56211200	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:56192400-56202200	Strong transcription	GM12878-XiMat	blood
29	chr19:56192400-56212400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr19:56192600-56209200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr19:56192800-56206200	Weak transcription	Psoas Muscle	Psoas
32	chr19:56192800-56213200	Strong transcription	Adipose Nuclei	Adipose
33	chr19:56193000-56204400	Weak transcription	NH-A	brain
34	chr19:56193200-56214000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:56193600-56213200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:56193800-56212000	Weak transcription	HSMM	muscle
37	chr19:56194000-56209600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:56194600-56209800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:56194800-56208400	Strong transcription	NHLF	lung
40	chr19:56195000-56208400	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr19:56195000-56210000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:56195000-56210200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr19:56195000-56212400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:56195400-56208000	Weak transcription	Fetal Kidney	kidney
45	chr19:56195400-56217600	Weak transcription	Right Atrium	heart
46	chr19:56195600-56204600	Weak transcription	Hela-S3	cervix
47	chr19:56195800-56210000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:56196000-56202400	Genic enhancers	Fetal Intestine Small	intestine
49	chr19:56196000-56208000	Strong transcription	Fetal Lung	lung
50	chr19:56196200-56210200	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links