Variant report

Variant	rs2682547
Chromosome Location	chr19:44001057-44001058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2682550	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213255	0.84[CEU][hapmap]
rs3213263	0.80[CEU][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2682547	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs2682547	PVRL2	cis	cerebellum	SCAN
rs2682547	ZNF649	cis	parietal	SCAN
rs2682547	TRPM4	cis	cerebellum	SCAN
rs2682547	BCAT2	cis	cerebellum	SCAN
rs2682547	SLC17A7	cis	cerebellum	SCAN
rs2682547	IZUMO1	cis	cerebellum	SCAN
rs2682547	BLOC1S3	cis	parietal	SCAN
rs2682547	XRCC1	cis	lymphoblastoid	seeQTL
rs2682547	ZNF575	cis	lung	GTEx
rs2682547	BCAT2	cis	parietal	SCAN
rs2682547	SLC8A2	cis	cerebellum	SCAN

Chromatin state (count:113 , 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	chr19:43980000-44001200	Weak transcription	Brain Substantia Nigra	brain
3	chr19:43980000-44001200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:43980000-44005600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr19:43980000-44005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr19:43980000-44006200	Weak transcription	HMEC	breast
7	chr19:43980400-44001200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:43980800-44007400	Weak transcription	HSMM	muscle
9	chr19:43981200-44007200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:43981400-44007200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr19:43982800-44006800	Weak transcription	K562	blood
12	chr19:43983600-44005800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:43988000-44004400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:43993000-44005600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:43993000-44007200	Weak transcription	A549	lung
16	chr19:43993600-44005800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:43993600-44006200	Weak transcription	GM12878-XiMat	blood
18	chr19:43993600-44007400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:43994200-44007200	Weak transcription	Primary B cells from cord blood	blood
20	chr19:43994400-44001800	Strong transcription	Fetal Stomach	stomach
21	chr19:43994800-44002600	Strong transcription	Fetal Intestine Large	intestine
22	chr19:43994800-44002800	Strong transcription	Fetal Intestine Small	intestine
23	chr19:43996000-44006400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:43997000-44001200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr19:43997400-44002800	Weak transcription	Stomach Mucosa	stomach
26	chr19:43997400-44003600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:43997400-44007000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:43997600-44001800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:43997600-44002400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr19:43997600-44003000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:43997600-44003800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:43997600-44003800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:43997600-44004200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr19:43997600-44004800	Strong transcription	Primary T cells from cord blood	blood
35	chr19:43997600-44006200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:43998000-44001200	Strong transcription	Liver	Liver
37	chr19:43998000-44001600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:43998000-44002800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:43998000-44007200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:43998200-44002200	Strong transcription	Gastric	stomach
41	chr19:43998200-44002800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:43998200-44003200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:43998200-44003600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:43998200-44003600	Strong transcription	Thymus	Thymus
45	chr19:43998200-44003800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:43998200-44006200	Weak transcription	Dnd41	blood
47	chr19:43998400-44001600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:43998400-44001600	Strong transcription	Fetal Muscle Leg	muscle
49	chr19:43998400-44003800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:43998400-44006000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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