Variant report

Variant	rs11666281
Chromosome Location	chr19:18234588-18234589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18208511..18210573-chr19:18234257..18236552,2	MCF-7	breast:
2	chr19:18234125..18236161-chr19:18252145..18256063,3	K562	blood:
3	chr19:18234013..18236269-chr19:18390865..18392530,3	MCF-7	breast:
4	chr19:18234373..18235964-chr19:18262195..18265012,2	K562	blood:
5	chr19:18234373..18236615-chr19:18262195..18264939,2	K562	blood:
6	chr19:18234040..18236524-chr19:18282001..18284422,2	K562	blood:

Variant related genes	Relation type
ENSG00000130522	Chromatin interaction
ENSG00000105647	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000096996	Chromatin interaction
ENSG00000216490	Chromatin interaction
ENSG00000269145	Chromatin interaction
ENSG00000099308	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11554159	0.86[CEU][hapmap]
rs11666424	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11666906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11668601	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs273488	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs273492	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs273507	0.86[ASN][1000 genomes]
rs273510	0.86[ASN][1000 genomes]
rs4808114	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808115	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4808745	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808751	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56252442	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56345159	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60146811	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66464318	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67234314	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72999447	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72999466	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs874628	0.81[CEU][hapmap]
rs885683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
5	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	esv1834142	chr19:18224729-18234588	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	nsv911246	chr19:18224729-18283501	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv911247	chr19:18224729-18288069	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
17	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised 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	37 gene(s)	inside rSNPs	diseases
19	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
20	nsv2429	chr19:18234179-18279381	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv911252	chr19:18234588-18338101	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11666281	KLHL26	cis	cerebellum	SCAN
rs11666281	MAST3	cis	parietal	SCAN
rs11666281	KIAA1683	cis	cerebellum	SCAN
rs11666281	F2RL3	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18229400-18234600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:18229400-18235000	Weak transcription	HSMMtube	muscle
3	chr19:18229400-18243000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:18229600-18237000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:18229800-18239000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:18229800-18239000	Weak transcription	Left Ventricle	heart
7	chr19:18229800-18241400	Weak transcription	HSMM	muscle
8	chr19:18229800-18243000	Weak transcription	Fetal Kidney	kidney
9	chr19:18230000-18235000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:18230000-18239600	Weak transcription	Osteobl	bone
11	chr19:18230000-18241400	Weak transcription	NHDF-Ad	bronchial
12	chr19:18230200-18235200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:18230200-18239400	Weak transcription	Right Ventricle	heart
14	chr19:18230200-18241200	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:18230200-18246600	Weak transcription	Hela-S3	cervix
16	chr19:18230200-18247200	Weak transcription	NHEK	skin
17	chr19:18230400-18236000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr19:18230400-18239400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:18230600-18236800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:18230600-18243000	Weak transcription	K562	blood
21	chr19:18230800-18239400	Weak transcription	Stomach Mucosa	stomach
22	chr19:18230800-18246200	Strong transcription	Fetal Intestine Small	intestine
23	chr19:18230800-18262000	Weak transcription	Dnd41	blood
24	chr19:18231000-18243000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:18231000-18243000	Weak transcription	Fetal Brain Male	brain
26	chr19:18231000-18262200	Weak transcription	HMEC	breast
27	chr19:18231400-18262200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr19:18231400-18262400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr19:18231600-18235000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:18231800-18235600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:18231800-18246200	Strong transcription	Fetal Intestine Large	intestine
32	chr19:18232000-18236000	Strong transcription	GM12878-XiMat	blood
33	chr19:18232000-18237400	Strong transcription	Brain Cingulate Gyrus	brain
34	chr19:18232000-18238800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:18232000-18244000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:18232000-18262200	Strong transcription	Brain Hippocampus Middle	brain
37	chr19:18232200-18235000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:18232200-18235400	Genic enhancers	Spleen	Spleen
39	chr19:18232200-18235600	Strong transcription	Colonic Mucosa	Colon
40	chr19:18232200-18237400	Strong transcription	Primary T cells from cord blood	blood
41	chr19:18232200-18237400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:18232200-18237600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:18232200-18237800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:18232200-18237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:18232200-18237800	Strong transcription	Liver	Liver
46	chr19:18232200-18237800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:18232200-18238400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:18232200-18246400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr19:18232200-18260000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:18232200-18260000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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