Variant report

Variant	rs1530500
Chromosome Location	chr19:37823811-37823812
allele	A/G
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	GATA3	chr19:37823729-37823953	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37740273..37743128-chr19:37823150..37825762,2	MCF-7	breast:
2	chr19:37822549..37827431-chr19:37836072..37838954,4	MCF-7	breast:

Variant related genes	Relation type
HKR1	TF binding region
ENSG00000267682	TF binding region
ENSG00000181666	Chromatin interaction
ENSG00000226686	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10418740	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1236810	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs1465434	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs256737	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256739	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256742	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256743	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2617789	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap]
rs2972596	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs320886	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs45483504	0.83[EUR][1000 genomes]
rs62110388	0.80[EUR][1000 genomes]
rs62110389	0.83[EUR][1000 genomes]
rs62110390	0.83[EUR][1000 genomes]
rs62110392	0.80[EUR][1000 genomes]
rs6508729	1.00[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs7251097	0.87[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7258906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73027379	0.81[EUR][1000 genomes]
rs7408736	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv978812	chr19:37821277-37824004	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1530500	ITPKC	cis	cerebellum	SCAN
rs1530500	EXOSC5	cis	cerebellum	SCAN
rs1530500	CATSPERG	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37809200-37824800	Weak transcription	Stomach Mucosa	stomach
2	chr19:37809400-37825000	Weak transcription	Fetal Thymus	thymus
3	chr19:37809400-37825000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:37809600-37824400	Weak transcription	NHDF-Ad	bronchial
5	chr19:37809600-37825000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:37810000-37825000	Weak transcription	Hela-S3	cervix
7	chr19:37810600-37824400	Weak transcription	Small Intestine	intestine
8	chr19:37810600-37824800	Weak transcription	Fetal Heart	heart
9	chr19:37810800-37824200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:37811600-37825000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:37815000-37824800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr19:37816800-37825000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:37817000-37825000	Weak transcription	Gastric	stomach
14	chr19:37817200-37824800	Weak transcription	Psoas Muscle	Psoas
15	chr19:37819200-37824800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:37819400-37824800	Weak transcription	Fetal Intestine Small	intestine
17	chr19:37820000-37825200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:37820200-37824800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:37820200-37824800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:37820400-37824400	Weak transcription	Colonic Mucosa	Colon
21	chr19:37820400-37824800	Weak transcription	Esophagus	oesophagus
22	chr19:37820400-37824800	Weak transcription	Fetal Brain Female	brain
23	chr19:37820400-37825000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:37820400-37825000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:37820400-37825000	Weak transcription	Fetal Lung	lung
26	chr19:37820600-37824200	Weak transcription	HepG2	liver
27	chr19:37820600-37824800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr19:37820600-37824800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:37820600-37824800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:37820600-37825000	Weak transcription	HSMMtube	muscle
31	chr19:37820800-37824200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:37820800-37824400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:37820800-37824800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:37820800-37824800	Weak transcription	Brain Angular Gyrus	brain
35	chr19:37820800-37824800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:37820800-37824800	Weak transcription	Brain Germinal Matrix	brain
37	chr19:37820800-37824800	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:37820800-37824800	Weak transcription	Colon Smooth Muscle	Colon
39	chr19:37820800-37824800	Weak transcription	Pancreas	Pancrea
40	chr19:37820800-37825000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr19:37820800-37825000	Weak transcription	Spleen	Spleen
42	chr19:37820800-37825000	Weak transcription	NHLF	lung
43	chr19:37821000-37824400	Weak transcription	Osteobl	bone
44	chr19:37821000-37824600	Weak transcription	HMEC	breast
45	chr19:37821000-37824800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:37821000-37825000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr19:37821000-37825000	Weak transcription	HSMM	muscle
48	chr19:37821000-37825200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:37821000-37825200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:37821200-37824800	Weak transcription	Left Ventricle	heart

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