Variant report

Variant	rs10401227
Chromosome Location	chr19:55614574-55614575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55609257..55613232-chr19:55613674..55618222,6	K562	blood:
2	chr19:55611452..55618868-chr19:55626160..55631612,12	K562	blood:
3	chr14:103799761..103800266-chr19:55614152..55614910,2	Hela-S3	cervix:
4	chr19:55605766..55607789-chr19:55614065..55616285,2	K562	blood:
5	chr19:55613614..55616655-chr19:55626160..55629067,3	K562	blood:
6	chr19:55610882..55614666-chr19:55626430..55628703,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100664	Chromatin interaction
ENSG00000125503	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12982674	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12982699	0.85[EUR][1000 genomes]
rs2109067	0.93[ASN][1000 genomes]
rs2532059	0.99[ASN][1000 genomes]
rs34374641	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56350931	0.86[EUR][1000 genomes]
rs57104390	0.80[ASN][1000 genomes]
rs66707428	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7253188	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7259963	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv1063666	chr19:55030439-55622780	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv817874	chr19:55595687-55614923	Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv912449	chr19:55595687-55630425	Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv912450	chr19:55595687-55633043	Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription 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	30 gene(s)	inside rSNPs	diseases
6	nsv912452	chr19:55595687-55644325	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1055961	chr19:55613727-55644076	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55593800-55620400	Weak transcription	HMEC	breast
2	chr19:55599200-55626600	Weak transcription	Fetal Kidney	kidney
3	chr19:55599200-55627200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:55599400-55614800	Weak transcription	GM12878-XiMat	blood
5	chr19:55599800-55626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:55600000-55614600	Weak transcription	HSMM	muscle
7	chr19:55600000-55626600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:55600000-55627000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:55600200-55614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:55600600-55614600	Weak transcription	HUVEC	blood vessel
11	chr19:55601400-55626400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:55602000-55615400	Strong transcription	Lung	lung
13	chr19:55602000-55618400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:55602800-55626400	Weak transcription	Hela-S3	cervix
15	chr19:55606400-55621600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:55606600-55627200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:55607000-55614800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:55607600-55624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:55607800-55614800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:55609000-55614600	Strong transcription	Adipose Nuclei	Adipose
21	chr19:55609000-55614800	Strong transcription	Esophagus	oesophagus
22	chr19:55609000-55616000	Strong transcription	Colon Smooth Muscle	Colon
23	chr19:55609000-55618400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:55609200-55615000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr19:55609200-55615200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr19:55609200-55615200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr19:55609400-55614600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:55609400-55614600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr19:55609400-55614600	Strong transcription	Fetal Intestine Large	intestine
30	chr19:55609400-55614600	Strong transcription	Thymus	Thymus
31	chr19:55609400-55614800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:55609400-55614800	Strong transcription	Fetal Thymus	thymus
33	chr19:55609400-55615200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:55609400-55615200	Strong transcription	Liver	Liver
35	chr19:55609400-55618400	Strong transcription	Dnd41	blood
36	chr19:55609600-55614600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr19:55609600-55614600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:55609600-55614600	Strong transcription	Osteobl	bone
39	chr19:55609600-55615200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr19:55609800-55614800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:55610000-55615200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr19:55610000-55615200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:55610000-55615200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:55610600-55614600	Weak transcription	Fetal Brain Male	brain
45	chr19:55611000-55614600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:55611000-55615000	Weak transcription	Stomach Mucosa	stomach
47	chr19:55611000-55615200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr19:55611400-55618800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr19:55611600-55614600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:55611600-55623000	Weak transcription	Right Atrium	heart

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