Variant report

Variant	rs2700424
Chromosome Location	chr3:121649477-121649478
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10934568	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11916150	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490565	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12695420	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13068522	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474327	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1589700	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2091665	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2141614	0.81[JPT][hapmap]
rs2332056	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs2689276	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34227248	0.82[AMR][1000 genomes]
rs3817599	0.89[CEU][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4419417	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6438689	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770115	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6770719	0.81[JPT][hapmap]
rs6780559	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73181839	0.82[AMR][1000 genomes]
rs7626740	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7628167	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7638094	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7646346	0.82[CHB][hapmap]
rs7647751	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289184	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289185	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs953730	0.81[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9815649	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828757	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9829181	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9843053	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv877384	chr3:121601577-121659774	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2700424	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121615800-121671600	Weak transcription	Pancreas	Pancrea
2	chr3:121616200-121659400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:121625000-121661200	Weak transcription	Thymus	Thymus
4	chr3:121626200-121651600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr3:121627400-121659200	Weak transcription	Lung	lung
6	chr3:121627400-121664600	Weak transcription	Aorta	Aorta
7	chr3:121627600-121659200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:121628200-121659200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:121629800-121651400	Strong transcription	Primary B cells from cord blood	blood
10	chr3:121630200-121652200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:121630400-121649600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:121631800-121664800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:121633200-121661200	Weak transcription	Liver	Liver
14	chr3:121633800-121661200	Weak transcription	Right Ventricle	heart
15	chr3:121634000-121651400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:121634000-121651600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:121634000-121660400	Weak transcription	Fetal Kidney	kidney
18	chr3:121634800-121649600	Weak transcription	Brain Anterior Caudate	brain
19	chr3:121634800-121667000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:121635000-121670600	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:121635200-121666800	Weak transcription	Brain Substantia Nigra	brain
22	chr3:121638400-121664800	Weak transcription	Spleen	Spleen
23	chr3:121638600-121661000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:121638800-121661000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:121640800-121651400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:121640800-121659400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:121642400-121661600	Weak transcription	Fetal Thymus	thymus
28	chr3:121643400-121659200	Weak transcription	Fetal Lung	lung
29	chr3:121644000-121661200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:121644400-121651400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:121645600-121649800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:121646600-121661800	Weak transcription	Ovary	ovary
33	chr3:121646800-121666200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:121647200-121659400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:121647200-121660600	Weak transcription	Small Intestine	intestine
36	chr3:121647400-121651200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:121647400-121651400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr3:121647400-121651800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:121647400-121652000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:121647400-121659200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:121648000-121650400	Weak transcription	Psoas Muscle	Psoas
42	chr3:121648200-121649800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:121648200-121650200	Weak transcription	Primary T cells from cord blood	blood
44	chr3:121648400-121651600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:121648400-121658000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:121648800-121657800	Weak transcription	GM12878-XiMat	blood
47	chr3:121648800-121659800	Weak transcription	Left Ventricle	heart
48	chr3:121649000-121650600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:121649200-121650400	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:121649200-121658200	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links