Variant report

Variant	rs16924899
Chromosome Location	chr11:17095596-17095597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17094856..17097184-chr11:17228610..17231252,2	K562	blood:
2	chr11:17094939..17099575-chr11:17373026..17376765,6	K562	blood:
3	chr11:16847181..16850081-chr11:17095305..17097165,2	K562	blood:

Variant related genes	Relation type
ENSG00000011405	Chromatin interaction
ENSG00000188211	Chromatin interaction
ENSG00000070081	Chromatin interaction
ENSG00000166689	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11024180	0.82[ASN][1000 genomes]
rs11600230	1.00[ASN][1000 genomes]
rs11603765	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11604470	1.00[CHB][hapmap]
rs11604561	1.00[CHB][hapmap]
rs11605718	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11607974	1.00[CHB][hapmap]
rs11826970	0.82[ASN][1000 genomes]
rs12419179	1.00[ASN][1000 genomes]
rs1471980	1.00[ASN][1000 genomes]
rs16933823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16933827	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16933873	1.00[ASN][1000 genomes]
rs17647408	1.00[CHB][hapmap]
rs1967077	1.00[ASN][1000 genomes]
rs1974527	1.00[ASN][1000 genomes]
rs1979602	1.00[CHB][hapmap]
rs2040859	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28845191	1.00[ASN][1000 genomes]
rs35493302	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57726107	1.00[ASN][1000 genomes]
rs59545597	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60698184	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61879689	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61879695	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61879701	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][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	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers 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	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16924899	MYOD1	cis	parietal	SCAN
rs16924899	NUCB2	cis	cerebellum	SCAN
rs16924899	TMEM86A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17069400-17096200	Weak transcription	Pancreas	Pancrea
2	chr11:17085400-17097200	Weak transcription	Right Ventricle	heart
3	chr11:17085400-17098200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:17087000-17098000	Weak transcription	Esophagus	oesophagus
5	chr11:17088600-17095800	Weak transcription	Brain Angular Gyrus	brain
6	chr11:17088600-17096400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:17089400-17097600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:17092200-17096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:17092200-17096400	Strong transcription	Fetal Brain Female	brain
10	chr11:17092200-17098200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:17092200-17098200	Weak transcription	Aorta	Aorta
12	chr11:17092400-17095800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:17092600-17096200	Strong transcription	Placenta	Placenta
14	chr11:17092800-17096400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:17092800-17097600	Weak transcription	Colonic Mucosa	Colon
16	chr11:17093400-17095600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:17093400-17097200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:17093600-17096200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:17093600-17096200	Weak transcription	Gastric	stomach
20	chr11:17093600-17096400	Strong transcription	Fetal Muscle Leg	muscle
21	chr11:17093600-17097200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:17093600-17097200	Strong transcription	Fetal Stomach	stomach
23	chr11:17093800-17095800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:17093800-17096000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr11:17093800-17096000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:17093800-17096400	Weak transcription	Small Intestine	intestine
27	chr11:17093800-17096600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr11:17093800-17097200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:17093800-17097600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr11:17094000-17095600	Weak transcription	Fetal Heart	heart
31	chr11:17094000-17096200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:17094000-17096400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:17094000-17096400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:17094000-17097400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:17094200-17096600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr11:17094400-17096200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:17094400-17096200	Weak transcription	Thymus	Thymus
38	chr11:17094400-17096600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:17094400-17096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:17094400-17097200	Strong transcription	Fetal Intestine Large	intestine
41	chr11:17094600-17095600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:17094600-17095600	Strong transcription	Liver	Liver
43	chr11:17094600-17096400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:17094600-17096400	Strong transcription	Primary B cells from cord blood	blood
45	chr11:17094600-17096400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr11:17094600-17096400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr11:17094600-17096400	Strong transcription	Dnd41	blood
48	chr11:17094600-17096400	Strong transcription	NHEK	skin
49	chr11:17094600-17096400	Strong transcription	Osteobl	bone
50	chr11:17094600-17096600	Strong transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links