Variant report

Variant	rs2553430
Chromosome Location	chr3:101089262-101089263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1019677	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs10936607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10936642	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10936664	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12491955	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12496260	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13087404	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13088318	0.85[CEU][hapmap]
rs13089177	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs13089552	0.86[ASN][1000 genomes]
rs13320918	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13322987	0.94[EUR][1000 genomes]
rs16843927	1.00[CEU][hapmap];0.91[YRI][hapmap];0.95[EUR][1000 genomes]
rs1918405	0.89[EUR][1000 genomes]
rs2141179	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2141180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2178036	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2250611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2317699	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2317700	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2317749	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2317751	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2433031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2553416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2553424	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682383	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682391	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28565548	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34255148	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs348866	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs348869	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs3846091	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4287896	0.89[EUR][1000 genomes]
rs4456838	0.84[EUR][1000 genomes]
rs4524254	0.84[EUR][1000 genomes]
rs4683899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683917	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683918	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs473702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs487623	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs497953	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs503734	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs508537	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs520558	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs533852	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs551442	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56075912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62280667	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441602	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441608	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441610	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6771561	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6772703	1.00[CEU][hapmap];0.86[YRI][hapmap];0.93[EUR][1000 genomes]
rs6773536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7628681	0.89[EUR][1000 genomes]
rs7631506	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes]
rs7636475	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9814991	0.90[EUR][1000 genomes]
rs9843186	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9856435	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859077	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9870114	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9874188	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	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
rs2553430	SENP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101030800-101096400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:101038600-101101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:101038800-101089800	Weak transcription	Pancreas	Pancrea
4	chr3:101039800-101106600	Weak transcription	Thymus	Thymus
5	chr3:101040800-101090000	Weak transcription	Brain Angular Gyrus	brain
6	chr3:101042800-101089600	Weak transcription	NH-A	brain
7	chr3:101043200-101105000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:101043800-101096600	Weak transcription	Brain Substantia Nigra	brain
9	chr3:101044400-101103000	Weak transcription	Gastric	stomach
10	chr3:101045800-101110800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:101047400-101096000	Weak transcription	Psoas Muscle	Psoas
12	chr3:101049200-101096000	Weak transcription	Ovary	ovary
13	chr3:101049200-101102200	Weak transcription	Right Ventricle	heart
14	chr3:101066000-101089800	Weak transcription	Brain Germinal Matrix	brain
15	chr3:101066000-101094000	Weak transcription	Fetal Intestine Large	intestine
16	chr3:101066200-101095400	Weak transcription	Fetal Kidney	kidney
17	chr3:101066200-101096000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:101069000-101089800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:101073200-101091000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:101074600-101092200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:101076200-101102000	Weak transcription	Lung	lung
22	chr3:101076200-101105600	Weak transcription	Esophagus	oesophagus
23	chr3:101076600-101091400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:101076600-101096400	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:101076800-101092800	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:101076800-101093400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:101077000-101095800	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:101077000-101096000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:101077000-101102200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:101077800-101094400	Weak transcription	Fetal Intestine Small	intestine
31	chr3:101077800-101096000	Weak transcription	Small Intestine	intestine
32	chr3:101077800-101101000	Weak transcription	NHDF-Ad	bronchial
33	chr3:101077800-101102000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:101078200-101093200	Weak transcription	GM12878-XiMat	blood
35	chr3:101079000-101090800	Strong transcription	Primary B cells from cord blood	blood
36	chr3:101079200-101096000	Weak transcription	HSMMtube	muscle
37	chr3:101079600-101094400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:101080400-101098800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:101081200-101091000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:101081200-101091000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:101081200-101094600	Weak transcription	Stomach Mucosa	stomach
42	chr3:101083200-101089800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:101083200-101102000	Weak transcription	Left Ventricle	heart
44	chr3:101083400-101089800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:101083400-101101800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:101083400-101105200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:101083600-101090800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:101083600-101094400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:101083600-101096400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:101083600-101098200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links