Variant report

Variant	rs2203990
Chromosome Location	chr19:44017925-44017926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12978269	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2261316	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305375	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2355994	0.83[EUR][1000 genomes]
rs2599445	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2599447	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2599454	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2599455	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2599456	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2682553	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2682566	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2682578	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682579	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6509092	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6509096	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7252955	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110232	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44009000-44023600	Weak transcription	Stomach Mucosa	stomach
2	chr19:44009200-44029200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:44009200-44029600	Weak transcription	Psoas Muscle	Psoas
4	chr19:44009400-44018200	Weak transcription	Fetal Brain Male	brain
5	chr19:44009400-44018200	Weak transcription	Pancreas	Pancrea
6	chr19:44009400-44018400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:44009400-44018400	Weak transcription	Right Ventricle	heart
8	chr19:44009400-44020200	Weak transcription	Right Atrium	heart
9	chr19:44009400-44022000	Weak transcription	Primary B cells from cord blood	blood
10	chr19:44009400-44023600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:44009600-44023400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr19:44009600-44023600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:44009600-44023600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:44009800-44019800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:44009800-44021600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:44010000-44021800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:44010200-44021600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:44010200-44023400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:44010400-44018600	Weak transcription	HUVEC	blood vessel
20	chr19:44010400-44023000	Weak transcription	Hela-S3	cervix
21	chr19:44010400-44023400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:44010400-44023600	Weak transcription	K562	blood
23	chr19:44011200-44029400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:44012800-44021600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:44013000-44028600	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:44013000-44028800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:44013200-44020000	Weak transcription	HSMM	muscle
28	chr19:44013200-44023400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:44013200-44028600	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:44013200-44029800	Weak transcription	Small Intestine	intestine
31	chr19:44013400-44023000	Weak transcription	NH-A	brain
32	chr19:44013400-44023800	Weak transcription	Fetal Lung	lung
33	chr19:44013400-44029400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr19:44013600-44023600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:44014400-44023200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:44014400-44023400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:44014400-44029400	Weak transcription	Dnd41	blood
38	chr19:44015000-44023000	Weak transcription	HSMMtube	muscle
39	chr19:44015200-44021000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:44015200-44028600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr19:44015200-44028800	Weak transcription	Gastric	stomach
42	chr19:44015400-44023400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr19:44015400-44023600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:44015400-44028400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:44015400-44028800	Weak transcription	Fetal Thymus	thymus
46	chr19:44015400-44028800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:44015400-44029000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:44015400-44029200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr19:44015400-44029400	Weak transcription	Brain Germinal Matrix	brain
50	chr19:44015400-44029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links