Variant report

Variant	rs10407230
Chromosome Location	chr19:38610670-38610671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10401829	1.00[AMR][1000 genomes]
rs10401835	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10402883	1.00[AMR][1000 genomes]
rs10403595	0.89[AFR][1000 genomes]
rs10403809	1.00[AMR][1000 genomes]
rs10404447	1.00[EUR][1000 genomes]
rs10405162	1.00[EUR][1000 genomes]
rs10405381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406765	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407169	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407370	1.00[EUR][1000 genomes]
rs10407806	1.00[EUR][1000 genomes]
rs10408169	1.00[EUR][1000 genomes]
rs10408479	1.00[AMR][1000 genomes]
rs10408909	1.00[AMR][1000 genomes]
rs10410961	1.00[EUR][1000 genomes]
rs10412116	1.00[AMR][1000 genomes]
rs10413138	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413363	1.00[AMR][1000 genomes]
rs10413551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413596	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413865	1.00[EUR][1000 genomes]
rs10414605	1.00[EUR][1000 genomes]
rs10414916	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414927	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10415289	1.00[EUR][1000 genomes]
rs10415809	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419299	1.00[EUR][1000 genomes]
rs10419700	1.00[EUR][1000 genomes]
rs10419708	1.00[EUR][1000 genomes]
rs10419753	1.00[EUR][1000 genomes]
rs10420885	1.00[EUR][1000 genomes]
rs10421241	1.00[AMR][1000 genomes]
rs10423429	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424104	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424626	1.00[EUR][1000 genomes]
rs10424818	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10425099	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10425571	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426292	1.00[AMR][1000 genomes]
rs10426458	1.00[AMR][1000 genomes]
rs13343460	1.00[EUR][1000 genomes]
rs28376501	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28380555	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28421402	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28516776	1.00[EUR][1000 genomes]
rs28540039	1.00[EUR][1000 genomes]
rs28625002	1.00[EUR][1000 genomes]
rs28627637	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637743	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28649033	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28660098	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28700884	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134404	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56216562	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58260561	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59501312	1.00[EUR][1000 genomes]
rs59571293	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61456950	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71354969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73630898	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73632925	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73632930	0.93[AFR][1000 genomes]
rs73930357	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930389	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv1804371	chr19:38610640-38616928	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
4	chr19:38590200-38611000	Strong transcription	Duodenum Smooth Muscle	Duodenum
5	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
6	chr19:38596000-38613800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:38597800-38611800	Strong transcription	Osteobl	bone
8	chr19:38597800-38612000	Strong transcription	HSMM	muscle
9	chr19:38598200-38611800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
11	chr19:38602800-38612800	Weak transcription	Hela-S3	cervix
12	chr19:38603000-38611200	Weak transcription	Fetal Brain Male	brain
13	chr19:38603000-38625400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:38603200-38611200	Weak transcription	Fetal Heart	heart
15	chr19:38604000-38613400	Strong transcription	Primary B cells from cord blood	blood
16	chr19:38605800-38625400	Weak transcription	HMEC	breast
17	chr19:38606000-38613000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:38606200-38612000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr19:38606200-38612800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:38606200-38613800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:38607200-38613800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:38607600-38613200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr19:38607600-38613400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:38607600-38613800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:38607600-38613800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:38607800-38613800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:38608200-38611600	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr19:38608400-38611200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:38608400-38611600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr19:38608400-38611600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:38608400-38611800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:38608400-38613800	Strong transcription	Liver	Liver
33	chr19:38608600-38612000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:38608800-38611200	Strong transcription	Adipose Nuclei	Adipose
35	chr19:38608800-38611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr19:38608800-38613600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:38608800-38614000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:38608800-38614000	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr19:38609000-38611200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:38609000-38611800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:38609000-38611800	ZNF genes & repeats	Fetal Stomach	stomach
42	chr19:38609000-38611800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:38609200-38611200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:38609200-38611800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
45	chr19:38609400-38611000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr19:38609400-38611600	Strong transcription	Rectal Smooth Muscle	rectum
47	chr19:38609400-38611800	Strong transcription	Primary T cells from cord blood	blood
48	chr19:38609400-38611800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr19:38609400-38611800	Strong transcription	Brain Hippocampus Middle	brain
50	chr19:38609400-38611800	Strong transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links