Variant report

Variant	rs2399417
Chromosome Location	chr3:112067241-112067242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1050572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11921546	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12106675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859484	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817425	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4575866	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582023	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57404826	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59863561	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59981538	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60377655	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60497880	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60673403	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73856005	0.92[EUR][1000 genomes]
rs9842650	0.81[JPT][hapmap]

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:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112052800-112076200	Weak transcription	Right Ventricle	heart
2	chr3:112053200-112076400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:112054000-112068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:112054800-112076800	Weak transcription	Lung	lung
5	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:112055200-112068800	Weak transcription	Fetal Intestine Small	intestine
7	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:112055800-112076400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:112056600-112076400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:112057800-112068800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:112058600-112067400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:112058800-112069800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:112059200-112069000	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr3:112059600-112075000	Strong transcription	Fetal Thymus	thymus
15	chr3:112061200-112083000	Weak transcription	Colonic Mucosa	Colon
16	chr3:112061400-112076000	Strong transcription	Primary hematopoietic stem cells	blood
17	chr3:112061800-112067400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:112062200-112067800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:112062400-112069000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:112062400-112083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:112062600-112076600	Strong transcription	Primary B cells from cord blood	blood
22	chr3:112062800-112074600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:112063200-112067400	Strong transcription	Aorta	Aorta
24	chr3:112063400-112067400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:112063400-112074200	Strong transcription	Brain Germinal Matrix	brain
26	chr3:112063600-112068600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:112063800-112067600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:112064000-112076800	Weak transcription	Left Ventricle	heart
29	chr3:112064200-112074200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:112064200-112076800	Strong transcription	Placenta	Placenta
31	chr3:112064400-112075000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:112064400-112076800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:112064600-112068200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:112064800-112069400	Genic enhancers	GM12878-XiMat	blood
35	chr3:112064800-112069800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:112064800-112077200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:112065600-112068800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:112065600-112079600	Weak transcription	Fetal Intestine Large	intestine
39	chr3:112065800-112067400	Genic enhancers	Brain Hippocampus Middle	brain
40	chr3:112066000-112068200	Weak transcription	Right Atrium	heart
41	chr3:112066000-112089800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:112066200-112067400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:112066200-112068600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:112066200-112068800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:112066200-112073400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr3:112066400-112067400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:112066600-112071000	Enhancers	Brain Substantia Nigra	brain
48	chr3:112066600-112073600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
49	chr3:112066800-112067400	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr3:112066800-112067600	Strong transcription	Fetal Muscle Leg	muscle

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