Variant report

Variant	rs7253081
Chromosome Location	chr19:38201712-38201713
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1060522	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10853710	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083433	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11666172	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11668796	0.91[EUR][1000 genomes]
rs11671953	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11673497	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1291	0.96[YRI][hapmap]
rs16975299	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17246792	0.81[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28431170	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2891657	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34991303	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55871826	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55913702	0.91[EUR][1000 genomes]
rs55950325	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62108305	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62108351	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6508739	0.91[EUR][1000 genomes]
rs7249622	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258385	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7259272	0.81[YRI][hapmap]
rs73037060	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7253081	GSK3A	cis	parietal	SCAN
rs7253081	ZNF573	cis	multi-tissue	Pritchard
rs7253081	PHLDB3	cis	cerebellum	SCAN
rs7253081	AC012309.5	cis	Thyroid	GTEx
rs7253081	PSG11	cis	cerebellum	SCAN
rs7253081	PHLDB3	cis	parietal	SCAN
rs7253081	POU2F2	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
2	chr19:38184400-38208800	Weak transcription	HepG2	liver
3	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:38187400-38205800	Strong transcription	Dnd41	blood
6	chr19:38187400-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:38188200-38209200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38188400-38202000	Weak transcription	Placenta	Placenta
9	chr19:38189400-38209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:38190000-38206600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:38190600-38209000	Weak transcription	Brain Substantia Nigra	brain
12	chr19:38190600-38209200	Weak transcription	HSMMtube	muscle
13	chr19:38190800-38202200	Weak transcription	NH-A	brain
14	chr19:38190800-38209000	Weak transcription	Stomach Mucosa	stomach
15	chr19:38190800-38209200	Weak transcription	Fetal Thymus	thymus
16	chr19:38190800-38209200	Weak transcription	Psoas Muscle	Psoas
17	chr19:38191200-38209200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:38191200-38209200	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:38191600-38202000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:38192200-38203000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:38193800-38209000	Weak transcription	Hela-S3	cervix
22	chr19:38194000-38203000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:38194200-38202800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:38194600-38206600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:38195200-38204400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:38196000-38203000	ZNF genes & repeats	Liver	Liver
27	chr19:38196000-38204200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:38196200-38202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:38196200-38202600	Strong transcription	Left Ventricle	heart
30	chr19:38196200-38204400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr19:38196600-38202200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:38196600-38202200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr19:38196600-38202400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr19:38196800-38202800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr19:38197000-38203000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:38197000-38203000	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr19:38197200-38202800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:38197200-38203000	Strong transcription	Fetal Muscle Leg	muscle
39	chr19:38197200-38203400	Strong transcription	Primary T cells from cord blood	blood
40	chr19:38197400-38202800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr19:38197600-38201800	Strong transcription	Fetal Intestine Small	intestine
42	chr19:38197600-38208800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:38198400-38202600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:38198400-38202600	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr19:38198600-38204400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
46	chr19:38198800-38202000	Weak transcription	Brain Angular Gyrus	brain
47	chr19:38198800-38202000	Weak transcription	HMEC	breast
48	chr19:38198800-38202000	Weak transcription	NHEK	skin
49	chr19:38198800-38202200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:38198800-38202200	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links