Variant report

Variant	rs17513726
Chromosome Location	chr3:112078740-112078741
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11714917	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11716857	0.83[ASN][1000 genomes]
rs13073116	0.83[ASN][1000 genomes]
rs17447803	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17513698	0.88[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1996722	0.83[EUR][1000 genomes]
rs2280462	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2399411	0.83[ASN][1000 genomes]
rs2399426	0.82[EUR][1000 genomes]
rs4234416	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4550804	0.83[ASN][1000 genomes]
rs4682401	0.84[EUR][1000 genomes]
rs56037521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57785180	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62264131	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62264132	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62264133	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62264134	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438068	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6771014	0.83[ASN][1000 genomes]
rs6774405	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6785965	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73227438	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7611568	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7619941	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7621578	0.83[EUR][1000 genomes]
rs7653398	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs939576	0.83[ASN][1000 genomes]
rs939577	0.83[ASN][1000 genomes]
rs939578	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9814088	0.83[ASN][1000 genomes]
rs9818526	0.83[ASN][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:80 , 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	chr3:112065600-112079600	Weak transcription	Fetal Intestine Large	intestine
6	chr3:112066000-112089800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:112067000-112079400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:112067200-112079800	Weak transcription	Fetal Stomach	stomach
9	chr3:112067200-112080400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:112069200-112084000	Weak transcription	Fetal Kidney	kidney
11	chr3:112069200-112095400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:112070200-112086200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:112070600-112080400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:112070600-112080400	Weak transcription	Brain Anterior Caudate	brain
15	chr3:112070600-112086200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:112070600-112088800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:112070800-112079600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:112070800-112084600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:112070800-112090600	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:112071000-112083000	Weak transcription	Brain Substantia Nigra	brain
21	chr3:112071200-112083800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:112071800-112079400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:112072000-112080600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:112072400-112080400	Weak transcription	Fetal Brain Male	brain
25	chr3:112073000-112080400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:112073400-112079600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:112074200-112079600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:112077000-112079400	Weak transcription	Fetal Thymus	thymus
29	chr3:112077000-112079600	Weak transcription	Fetal Lung	lung
30	chr3:112077000-112083000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:112077200-112078800	Weak transcription	Placenta	Placenta
32	chr3:112077200-112079400	Weak transcription	Brain Germinal Matrix	brain
33	chr3:112077200-112079600	Weak transcription	Thymus	Thymus
34	chr3:112077200-112081200	Active TSS	Right Atrium	heart
35	chr3:112077200-112082000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:112077200-112094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:112077400-112079600	Weak transcription	Fetal Brain Female	brain
38	chr3:112077600-112079200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:112077600-112079400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:112077600-112079400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:112077600-112079600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:112077600-112079600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:112077600-112079800	Weak transcription	Left Ventricle	heart
44	chr3:112077600-112080400	Active TSS	Fetal Muscle Leg	muscle
45	chr3:112077600-112080400	Weak transcription	Psoas Muscle	Psoas
46	chr3:112077600-112080600	Weak transcription	Primary T cells from cord blood	blood
47	chr3:112077600-112082800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:112077600-112083000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:112077600-112107200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:112077800-112079000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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