Variant report

Variant	rs10420506
Chromosome Location	chr19:38670455-38670456
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10401165	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10403716	0.93[ASN][1000 genomes]
rs10412762	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10412865	0.93[ASN][1000 genomes]
rs10413751	0.81[JPT][hapmap]
rs10422665	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11083448	0.83[EUR][1000 genomes]
rs1614979	0.81[JPT][hapmap]
rs1654349	0.81[JPT][hapmap]
rs1654365	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1725475	0.81[JPT][hapmap]
rs1725512	0.81[JPT][hapmap]
rs2082442	0.93[ASN][1000 genomes]
rs2082443	0.93[ASN][1000 genomes]
rs28444246	0.93[EUR][1000 genomes]
rs28495744	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28581256	0.90[ASN][1000 genomes]
rs4802233	0.81[JPT][hapmap]
rs4802247	0.92[ASN][1000 genomes]
rs4802256	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802278	0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs4803786	0.87[ASN][1000 genomes]
rs4803809	0.93[ASN][1000 genomes]
rs4803810	0.93[ASN][1000 genomes]
rs4803828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803862	0.93[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap]
rs56166457	0.84[ASN][1000 genomes]
rs59185302	0.87[ASN][1000 genomes]
rs59579475	0.84[ASN][1000 genomes]
rs59924887	0.87[ASN][1000 genomes]
rs61388128	0.87[ASN][1000 genomes]
rs6508767	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7245788	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248428	0.90[ASN][1000 genomes]
rs7250034	0.93[ASN][1000 genomes]
rs7256332	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73627654	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73627663	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73627676	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73627686	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73930553	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8105468	0.87[ASN][1000 genomes]
rs855601	0.81[JPT][hapmap]
rs855603	0.81[JPT][hapmap]
rs855633	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs855636	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs855637	0.81[JPT][hapmap]
rs860623	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs863020	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs941039	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs941040	0.81[JPT][hapmap]
rs9941456	0.93[ASN][1000 genomes]
rs9941467	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[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	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
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10420506	CBLC	cis	parietal	SCAN
rs10420506	RINL	cis	cerebellum	SCAN
rs10420506	ZNF234	cis	parietal	SCAN
rs10420506	BCAM	cis	parietal	SCAN
rs10420506	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
2	chr19:38653800-38670800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38656200-38675200	Weak transcription	Stomach Mucosa	stomach
4	chr19:38656400-38670800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:38656400-38671400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:38656400-38674000	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:38657600-38673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38657600-38673800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:38657600-38696200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:38658400-38674000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:38658400-38684800	Weak transcription	HepG2	liver
12	chr19:38658400-38694000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr19:38658600-38670800	Weak transcription	Fetal Brain Female	brain
14	chr19:38659600-38673600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:38659600-38673600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:38659800-38670600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:38661000-38673200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:38661200-38670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:38661200-38671200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:38661200-38673600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:38661400-38682600	Weak transcription	Aorta	Aorta
22	chr19:38661600-38671600	Weak transcription	Osteobl	bone
23	chr19:38661600-38673600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:38661600-38674000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:38661800-38682400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:38663200-38673200	Weak transcription	Gastric	stomach
27	chr19:38663400-38671200	Weak transcription	Pancreas	Pancrea
28	chr19:38664400-38673200	Weak transcription	Colonic Mucosa	Colon
29	chr19:38664600-38674000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:38664600-38688600	Weak transcription	NH-A	brain
31	chr19:38664600-38699800	Weak transcription	Brain Substantia Nigra	brain
32	chr19:38664800-38673600	Weak transcription	Brain Anterior Caudate	brain
33	chr19:38664800-38674200	Weak transcription	Brain Hippocampus Middle	brain
34	chr19:38665000-38670800	Weak transcription	Brain Germinal Matrix	brain
35	chr19:38665000-38672800	Weak transcription	HSMMtube	muscle
36	chr19:38665000-38673200	Weak transcription	Esophagus	oesophagus
37	chr19:38665000-38684400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:38665200-38670600	Weak transcription	Left Ventricle	heart
39	chr19:38665200-38673200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:38665200-38674200	Weak transcription	Psoas Muscle	Psoas
41	chr19:38665200-38684200	Weak transcription	HMEC	breast
42	chr19:38666200-38682800	Weak transcription	Right Ventricle	heart
43	chr19:38666400-38671400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr19:38666400-38672800	Weak transcription	NHLF	lung
45	chr19:38666400-38673200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:38666400-38673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:38666400-38673400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:38666400-38673600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:38666600-38671400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:38667200-38673400	Weak transcription	NHEK	skin

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