Variant report

Variant	rs2682549
Chromosome Location	chr19:44001891-44001892
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	POLR2A	chr19:44001662-44001959	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
PHLDB3	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1125030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12978269	0.85[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs2261316	0.85[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap]
rs2305375	0.86[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap]
rs2599445	0.87[AFR][1000 genomes]
rs2599447	0.86[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs2599454	0.86[ASW][hapmap];0.88[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap]
rs2682545	0.90[ASN][1000 genomes]
rs2682578	0.85[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap]
rs34577669	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6509092	0.88[CEU][hapmap];0.95[YRI][hapmap]
rs6509096	0.88[CEU][hapmap];0.95[YRI][hapmap]
rs8110232	0.86[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv2762041	chr19:43986023-44014457	Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2682549	ZNF575	cis	lung	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43979600-44005800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:43980000-44005600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr19:43980000-44005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:43980000-44006200	Weak transcription	HMEC	breast
5	chr19:43980800-44007400	Weak transcription	HSMM	muscle
6	chr19:43981200-44007200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:43981400-44007200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:43982800-44006800	Weak transcription	K562	blood
9	chr19:43983600-44005800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:43988000-44004400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:43993000-44005600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:43993000-44007200	Weak transcription	A549	lung
13	chr19:43993600-44005800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:43993600-44006200	Weak transcription	GM12878-XiMat	blood
15	chr19:43993600-44007400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:43994200-44007200	Weak transcription	Primary B cells from cord blood	blood
17	chr19:43994800-44002600	Strong transcription	Fetal Intestine Large	intestine
18	chr19:43994800-44002800	Strong transcription	Fetal Intestine Small	intestine
19	chr19:43996000-44006400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:43997400-44002800	Weak transcription	Stomach Mucosa	stomach
21	chr19:43997400-44003600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr19:43997400-44007000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:43997600-44002400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:43997600-44003000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:43997600-44003800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:43997600-44003800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:43997600-44004200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr19:43997600-44004800	Strong transcription	Primary T cells from cord blood	blood
29	chr19:43997600-44006200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:43998000-44002800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:43998000-44007200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:43998200-44002200	Strong transcription	Gastric	stomach
33	chr19:43998200-44002800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:43998200-44003200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:43998200-44003600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:43998200-44003600	Strong transcription	Thymus	Thymus
37	chr19:43998200-44003800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:43998200-44006200	Weak transcription	Dnd41	blood
39	chr19:43998400-44003800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:43998400-44006000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:43998400-44006800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:43998600-44002000	Strong transcription	Lung	lung
43	chr19:43998600-44002000	Strong transcription	NHEK	skin
44	chr19:43998600-44002200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr19:43998600-44002600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr19:43998600-44002800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr19:43998600-44003600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr19:43998600-44005800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:43998800-44002000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:43998800-44002200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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