Variant report

Variant	rs10410924
Chromosome Location	chr19:39285451-39285452
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10411352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10422547	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10422733	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10423052	0.83[AMR][1000 genomes]
rs10423065	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10424200	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10424620	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11667079	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11669239	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001274	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4801877	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55647604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56265037	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57217905	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58406458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60800281	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7246540	0.81[AMR][1000 genomes]
rs7246893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247185	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108412	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109993	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8110778	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8111887	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8112427	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8112655	0.81[AMR][1000 genomes]
rs9749397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10410924	RNU6-140P	cis	Esophagus Mucosa	GTEx
rs10410924	LGALS7	cis	Esophagus Mucosa	GTEx
rs10410924	CAPN12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:54 , 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	chr19:39283200-39305600	Weak transcription	Brain Angular Gyrus	brain
4	chr19:39283200-39305600	Weak transcription	Brain Substantia Nigra	brain
5	chr19:39283400-39289600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr19:39283400-39291400	Weak transcription	Liver	Liver
7	chr19:39283400-39291600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr19:39283400-39294000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:39283400-39294000	Weak transcription	Pancreas	Pancrea
10	chr19:39283600-39291400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr19:39283600-39291800	Weak transcription	Gastric	stomach
12	chr19:39283600-39292200	Weak transcription	Right Ventricle	heart
13	chr19:39283600-39292600	Weak transcription	Colonic Mucosa	Colon
14	chr19:39283600-39294000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:39283600-39296000	Weak transcription	Left Ventricle	heart
16	chr19:39283600-39296000	Weak transcription	Lung	lung
17	chr19:39283600-39296000	Weak transcription	Right Atrium	heart
18	chr19:39283600-39305600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:39283600-39305800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:39283600-39305800	Weak transcription	Brain Hippocampus Middle	brain
21	chr19:39283600-39305800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr19:39283800-39289800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr19:39283800-39291400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:39283800-39291600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr19:39283800-39295800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:39283800-39295800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:39283800-39296000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr19:39283800-39306000	Weak transcription	Primary B cells from cord blood	blood
29	chr19:39284000-39288000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:39284000-39289600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:39284000-39291400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr19:39284000-39291600	Weak transcription	Primary T cells from cord blood	blood
33	chr19:39284000-39291600	Weak transcription	Adipose Nuclei	Adipose
34	chr19:39284000-39291800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:39284000-39295800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr19:39284000-39305600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:39284000-39318200	Weak transcription	Fetal Kidney	kidney
38	chr19:39284200-39289400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:39284200-39289400	Weak transcription	Fetal Intestine Small	intestine
40	chr19:39284200-39289600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr19:39284200-39291400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:39284200-39291800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:39284200-39294000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:39284200-39305800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr19:39284400-39289600	Weak transcription	Fetal Intestine Large	intestine
46	chr19:39284600-39289400	Weak transcription	Esophagus	oesophagus
47	chr19:39284600-39289600	Weak transcription	Placenta	Placenta
48	chr19:39284600-39289600	Weak transcription	NHEK	skin
49	chr19:39284600-39291600	Weak transcription	Spleen	Spleen
50	chr19:39284800-39289600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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