Variant report

Variant	rs2112799
Chromosome Location	chr19:56161206-56161207
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	POLR2A	chr19:56161189-56161239	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:56158704-56161230	GM19193	blood:	n/a	n/a
3	POLR2A	chr19:56158176-56161389	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56110653..56113509-chr19:56160158..56165183,5	MCF-7	breast:

Variant related genes	Relation type
U2AF2	TF binding region
ENSG00000179943	Chromatin interaction
ENSG00000171443	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11084406	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666362	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669614	1.00[LWK][hapmap]
rs11671023	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882068	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs3786650	1.00[ASN][1000 genomes]
rs4541174	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801261	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs4801278	1.00[LWK][hapmap]
rs73062531	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73062564	1.00[ASN][1000 genomes]
rs8104386	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
8	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2112799	CHMP2A	cis	parietal	SCAN
rs2112799	ZNF460	cis	parietal	SCAN
rs2112799	ZNF580	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56158200-56161800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:56160000-56162000	Flanking Active TSS	GM12878-XiMat	blood
3	chr19:56160000-56162800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:56160000-56165200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:56160200-56165200	Weak transcription	Small Intestine	intestine
6	chr19:56160400-56161600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:56160400-56161800	Enhancers	Lung	lung
8	chr19:56160400-56162400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:56160400-56163200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:56160400-56163400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:56160400-56163400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:56160400-56163400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:56160400-56164200	Weak transcription	Psoas Muscle	Psoas
14	chr19:56160400-56164400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:56160400-56164400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:56160400-56164400	Weak transcription	NHEK	skin
17	chr19:56160400-56165000	Weak transcription	HSMMtube	muscle
18	chr19:56160400-56165200	Weak transcription	NHDF-Ad	bronchial
19	chr19:56160600-56161400	Enhancers	Duodenum Mucosa	Duodenum
20	chr19:56160600-56161400	Genic enhancers	Fetal Muscle Leg	muscle
21	chr19:56160600-56161400	Enhancers	Fetal Thymus	thymus
22	chr19:56160600-56161600	Weak transcription	Thymus	Thymus
23	chr19:56160600-56161800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:56160600-56161800	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr19:56160600-56161800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr19:56160600-56161800	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr19:56160600-56162000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:56160600-56162200	Weak transcription	NH-A	brain
29	chr19:56160600-56163200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:56160600-56163400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:56160600-56164000	Weak transcription	Fetal Heart	heart
32	chr19:56160600-56164200	Weak transcription	HMEC	breast
33	chr19:56160600-56164400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr19:56160600-56164600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:56160600-56164600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:56160600-56164600	Weak transcription	Osteobl	bone
37	chr19:56160600-56164800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr19:56160800-56161400	Enhancers	Primary B cells from cord blood	blood
39	chr19:56160800-56161400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr19:56160800-56161400	Enhancers	Fetal Brain Male	brain
41	chr19:56160800-56161600	Weak transcription	Ovary	ovary
42	chr19:56160800-56161800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:56160800-56162400	Weak transcription	Esophagus	oesophagus
44	chr19:56160800-56163000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:56160800-56163400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:56160800-56163600	Weak transcription	Brain Germinal Matrix	brain
47	chr19:56160800-56163600	Weak transcription	Fetal Intestine Large	intestine
48	chr19:56160800-56164200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:56160800-56164400	Weak transcription	Hela-S3	cervix
50	chr19:56160800-56164400	Weak transcription	HepG2	liver

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