Variant report

Variant	rs3764576
Chromosome Location	chr19:22005000-22005001
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	chr19:22004997-22005120	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:22004785-22005104	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:22004889-22005122	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:22004773-22005313	K562	blood:	n/a	n/a
5	POLR2A	chr19:22004776-22005170	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:22004386-22005258	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:22004231..22005788-chr19:22018670..22020262,2	K562	blood:

Variant related genes	Relation type
ENSG00000268438	TF binding region
ENSG00000198521	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11085493	0.83[CHD][hapmap]
rs11671415	0.82[ASN][1000 genomes]
rs12460775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460998	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463030	0.82[ASN][1000 genomes]
rs12463064	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1510964	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17701305	1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs17701366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17701834	1.00[ASW][hapmap]
rs2136890	0.95[ASN][1000 genomes]
rs2435003	0.95[ASN][1000 genomes]
rs2435006	0.95[ASN][1000 genomes]
rs2435041	0.82[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2435044	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2457773	0.95[ASN][1000 genomes]
rs2457785	0.82[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2457802	0.95[ASN][1000 genomes]
rs56904798	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58664716	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60272092	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv833784	chr19:21902647-22037153	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1059079	chr19:21940891-22083420	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv578971	chr19:21950337-22008229	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv3395280	chr19:21968753-22202288	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv911428	chr19:21986292-22106951	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv911429	chr19:21986292-22110219	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv961194	chr19:21998424-22019912	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21985600-22011000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21988600-22018000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:21988800-22017200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:21989800-22013000	ZNF genes & repeats	Brain Germinal Matrix	brain
5	chr19:21990000-22005200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:21990800-22017600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr19:21991200-22010800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:21995000-22016600	Weak transcription	K562	blood
9	chr19:21999800-22008400	Weak transcription	Right Ventricle	heart
10	chr19:21999800-22009000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr19:21999800-22009400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:21999800-22018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:22000800-22007800	Weak transcription	Fetal Kidney	kidney
14	chr19:22000800-22008200	Weak transcription	HSMM	muscle
15	chr19:22000800-22008400	Weak transcription	Placenta	Placenta
16	chr19:22000800-22018200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:22000800-22018200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr19:22001000-22008400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:22001000-22012600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:22001000-22014000	Weak transcription	Psoas Muscle	Psoas
21	chr19:22001000-22018000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:22001000-22018000	Weak transcription	Brain Anterior Caudate	brain
23	chr19:22001000-22018000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr19:22001200-22009200	Weak transcription	Pancreas	Pancrea
25	chr19:22001200-22018200	Weak transcription	Gastric	stomach
26	chr19:22001400-22006400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:22001400-22009200	Weak transcription	Spleen	Spleen
28	chr19:22001400-22012600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:22001600-22008400	Weak transcription	Ovary	ovary
30	chr19:22001600-22008600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:22001800-22007000	Weak transcription	Osteobl	bone
32	chr19:22001800-22008400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:22002000-22006800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:22002000-22007200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:22002000-22007800	Weak transcription	Left Ventricle	heart
36	chr19:22002000-22014600	Weak transcription	NHLF	lung
37	chr19:22002000-22017800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr19:22002200-22005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:22002200-22005800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:22002200-22008600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr19:22002200-22009000	Weak transcription	Brain Hippocampus Middle	brain
42	chr19:22002400-22008200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:22002600-22005000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr19:22002600-22008200	Weak transcription	Adipose Nuclei	Adipose
45	chr19:22002600-22018000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:22002800-22007000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr19:22002800-22008200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr19:22002800-22008400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:22003400-22005200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:22003400-22005400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links