Variant report

Variant	rs10424620
Chromosome Location	chr19:39283767-39283768
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10410924	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10411352	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10422547	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422733	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423052	0.84[AMR][1000 genomes]
rs10423065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424200	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667079	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11669239	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801877	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55647604	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56265037	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57217905	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58406458	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60800281	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7246893	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7247185	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247475	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8108412	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109475	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8109993	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8110778	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111887	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8112427	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9749397	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9749398	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv1064688	chr19:39249059-39291526	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1061904	chr19:39249692-39302843	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv911671	chr19:39252238-39306425	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
8	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1063592	chr19:39257977-39287265	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv1058132	chr19:39279522-39302843	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv9721	chr19:39281857-39287128	Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10424620	CEACAM21	cis	cerebellum	SCAN
rs10424620	RNU6-140P	cis	Esophagus Mucosa	GTEx
rs10424620	LGALS7	cis	Esophagus Mucosa	GTEx
rs10424620	AXL	cis	cerebellum	SCAN
rs10424620	LYPD3	cis	cerebellum	SCAN
rs10424620	SYMPK	cis	cerebellum	SCAN
rs10424620	CAPN12	cis	Adipose Subcutaneous	GTEx
rs10424620	ERCC1	cis	cerebellum	SCAN
rs10424620	FOXA3	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39279800-39291600	Weak transcription	Stomach Mucosa	stomach
2	chr19:39282200-39291600	Weak transcription	Brain Anterior Caudate	brain
3	chr19:39282800-39283800	Enhancers	Primary B cells from cord blood	blood
4	chr19:39282800-39283800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:39282800-39284000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:39283000-39283800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr19:39283000-39283800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:39283000-39283800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr19:39283000-39283800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:39283000-39283800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr19:39283000-39283800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:39283000-39283800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:39283000-39283800	Flanking Active TSS	Esophagus	oesophagus
14	chr19:39283000-39283800	Bivalent Enhancer	Fetal Brain Male	brain
15	chr19:39283000-39283800	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr19:39283000-39283800	Active TSS	Rectal Smooth Muscle	rectum
17	chr19:39283000-39283800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr19:39283000-39284000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr19:39283000-39284000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:39283000-39284000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr19:39283000-39284200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr19:39283000-39284200	Enhancers	HUVEC	blood vessel
23	chr19:39283000-39284600	Enhancers	Spleen	Spleen
24	chr19:39283200-39283800	Enhancers	Colon Smooth Muscle	Colon
25	chr19:39283200-39283800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr19:39283200-39284000	Flanking Active TSS	NHEK	skin
27	chr19:39283200-39284200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:39283200-39284200	Enhancers	HepG2	liver
29	chr19:39283200-39284800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:39283200-39305600	Weak transcription	Brain Angular Gyrus	brain
31	chr19:39283200-39305600	Weak transcription	Brain Substantia Nigra	brain
32	chr19:39283400-39283800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:39283400-39283800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
34	chr19:39283400-39283800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr19:39283400-39283800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:39283400-39283800	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr19:39283400-39284000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr19:39283400-39284000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:39283400-39284000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:39283400-39284000	Enhancers	A549	lung
41	chr19:39283400-39284200	Enhancers	HSMM	muscle
42	chr19:39283400-39284400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr19:39283400-39289600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr19:39283400-39291400	Weak transcription	Liver	Liver
45	chr19:39283400-39291600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr19:39283400-39294000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:39283400-39294000	Weak transcription	Pancreas	Pancrea
48	chr19:39283600-39283800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:39283600-39283800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr19:39283600-39283800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links