Variant report

Variant	rs13090468
Chromosome Location	chr3:112077109-112077110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10511311	0.83[CEU][hapmap]
rs12106673	0.92[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs12106967	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs13069751	0.80[EUR][1000 genomes]
rs13070091	0.80[EUR][1000 genomes]
rs13098589	0.83[CEU][hapmap]
rs13100916	0.83[EUR][1000 genomes]
rs1317243	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs1879513	0.80[EUR][1000 genomes]
rs2272022	0.83[CEU][hapmap]
rs2399416	0.83[CEU][hapmap]
rs6438065	0.80[EUR][1000 genomes]
rs6762106	0.80[EUR][1000 genomes]
rs6773206	0.80[EUR][1000 genomes]
rs6798354	0.80[EUR][1000 genomes]
rs6798486	0.80[EUR][1000 genomes]
rs6805117	0.80[EUR][1000 genomes]
rs7647411	0.83[CEU][hapmap]
rs9814721	0.80[EUR][1000 genomes]
rs9852176	0.80[EUR][1000 genomes]
rs9856838	0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:112061200-112083000	Weak transcription	Colonic Mucosa	Colon
4	chr3:112062400-112083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112064800-112077200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:112065600-112079600	Weak transcription	Fetal Intestine Large	intestine
7	chr3:112066000-112089800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:112067000-112079400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:112067200-112079800	Weak transcription	Fetal Stomach	stomach
10	chr3:112067200-112080400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:112069200-112084000	Weak transcription	Fetal Kidney	kidney
12	chr3:112069200-112095400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:112070200-112086200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:112070600-112080400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:112070600-112080400	Weak transcription	Brain Anterior Caudate	brain
16	chr3:112070600-112086200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:112070600-112088800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:112070800-112079600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:112070800-112084600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:112070800-112090600	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:112071000-112077600	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:112071000-112083000	Weak transcription	Brain Substantia Nigra	brain
23	chr3:112071200-112083800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:112071800-112079400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:112072000-112080600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:112072400-112080400	Weak transcription	Fetal Brain Male	brain
27	chr3:112073000-112080400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:112073400-112079600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:112074200-112079600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:112074600-112078000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:112075000-112077400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:112075200-112078200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr3:112075600-112077200	Strong transcription	Brain Germinal Matrix	brain
34	chr3:112076000-112077400	Genic enhancers	Primary hematopoietic stem cells	blood
35	chr3:112076200-112077200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr3:112076200-112077200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:112076200-112077800	Active TSS	Right Ventricle	heart
38	chr3:112076200-112078200	Enhancers	Primary B cells from peripheral blood	blood
39	chr3:112076400-112077200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:112076400-112077200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:112076400-112077200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
42	chr3:112076400-112077600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr3:112076400-112077600	Enhancers	H9 Cell Line	embryonic stem cell
44	chr3:112076400-112078000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
45	chr3:112076400-112078000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr3:112076600-112077200	Genic enhancers	Primary B cells from cord blood	blood
47	chr3:112076600-112077600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:112076800-112077200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:112076800-112077200	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr3:112076800-112077200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links