Variant report

Variant	rs2290999
Chromosome Location	chr19:38138887-38138888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38085270..38087248-chr19:38138065..38140265,2	MCF-7	breast:
2	chr19:38137873..38139917-chr19:38145881..38147430,2	K562	blood:

Variant related genes	Relation type
ENSG00000171817	Chromatin interaction
ENSG00000180479	Chromatin interaction
ENSG00000120784	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11083427	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs11083428	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs11083430	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs1128327	0.90[JPT][hapmap]
rs11665759	0.92[EUR][1000 genomes]
rs11666662	1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11666738	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672440	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.89[ASN][1000 genomes]
rs12151280	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12162238	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs12459013	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12460230	0.81[JPT][hapmap]
rs12462505	0.94[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs1478462	1.00[EUR][1000 genomes]
rs17303301	0.90[JPT][hapmap]
rs17305326	0.99[EUR][1000 genomes]
rs2045911	0.95[EUR][1000 genomes]
rs2279150	0.90[JPT][hapmap]
rs241952	0.80[CEU][hapmap]
rs241955	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs35205379	1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs59426132	0.99[EUR][1000 genomes]
rs7248397	1.00[CEU][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes]
rs73031309	0.91[EUR][1000 genomes]
rs73031321	0.92[EUR][1000 genomes]
rs73031322	0.92[EUR][1000 genomes]
rs73031326	0.96[EUR][1000 genomes]
rs73033117	0.96[EUR][1000 genomes]
rs73033129	0.98[EUR][1000 genomes]
rs73033139	0.98[EUR][1000 genomes]
rs73033145	0.99[EUR][1000 genomes]
rs73035158	1.00[EUR][1000 genomes]
rs73035164	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73037036	1.00[EUR][1000 genomes]
rs73039018	0.87[EUR][1000 genomes]
rs73041004	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2290999	CATSPERG	cis	parietal	SCAN
rs2290999	CEACAM19	cis	cerebellum	SCAN
rs2290999	FOSB	cis	cerebellum	SCAN
rs2290999	PSMC4	cis	parietal	SCAN
rs2290999	PLEKHG2	cis	cerebellum	SCAN
rs2290999	EIF3K	cis	parietal	SCAN
rs2290999	MRPS12	cis	cerebellum	SCAN
rs2290999	ZFP112	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38121800-38139200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:38121800-38140600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:38123600-38140000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:38123600-38140800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:38123600-38141400	ZNF genes & repeats	Liver	Liver
6	chr19:38124600-38140800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:38124600-38142000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:38124800-38143200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:38124800-38144400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:38125600-38143200	ZNF genes & repeats	A549	lung
11	chr19:38125800-38139600	ZNF genes & repeats	Colon Smooth Muscle	Colon
12	chr19:38125800-38140800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
13	chr19:38126000-38141400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr19:38126200-38143200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:38126400-38139400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
16	chr19:38127200-38144600	Weak transcription	Hela-S3	cervix
17	chr19:38129200-38139600	Strong transcription	HSMM	muscle
18	chr19:38129600-38139000	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr19:38130000-38141600	Strong transcription	Osteobl	bone
20	chr19:38130400-38142200	ZNF genes & repeats	GM12878-XiMat	blood
21	chr19:38130600-38139800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:38131000-38139200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr19:38131000-38141000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:38131600-38139200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:38131600-38141200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:38131800-38139000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:38131800-38140600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr19:38132000-38139000	ZNF genes & repeats	Ovary	ovary
29	chr19:38132000-38139800	Strong transcription	Brain Cingulate Gyrus	brain
30	chr19:38132200-38139000	Strong transcription	Placenta	Placenta
31	chr19:38132200-38139200	Strong transcription	Brain Angular Gyrus	brain
32	chr19:38132200-38139400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr19:38132400-38139000	Strong transcription	Fetal Thymus	thymus
34	chr19:38132400-38139200	Strong transcription	Brain Substantia Nigra	brain
35	chr19:38132400-38139400	Strong transcription	Brain Hippocampus Middle	brain
36	chr19:38132600-38139200	Strong transcription	HepG2	liver
37	chr19:38133000-38139000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:38133000-38139200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr19:38133000-38139200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr19:38133000-38139200	Strong transcription	Fetal Muscle Leg	muscle
41	chr19:38133000-38139200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:38133000-38139600	Strong transcription	Fetal Brain Female	brain
43	chr19:38133000-38139800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr19:38133200-38139200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr19:38133400-38139200	Strong transcription	HUVEC	blood vessel
46	chr19:38133400-38140400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:38133600-38139200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
48	chr19:38133600-38140600	Strong transcription	Fetal Stomach	stomach
49	chr19:38133600-38140800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr19:38133600-38142000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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