Variant report

Variant	rs1540436
Chromosome Location	chr2:38811682-38811683
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38806614..38812442-chr2:38966843..38970976,5	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10495880	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12987111	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12990659	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991911	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs12995222	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12996029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431551	0.80[EUR][1000 genomes]
rs1368114	0.80[EUR][1000 genomes]
rs17421378	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs17421399	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17421503	0.93[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs17421545	0.85[ASN][1000 genomes]
rs17421587	0.82[EUR][1000 genomes]
rs17421743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17493321	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs17493363	0.88[CEU][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.84[ASN][1000 genomes]
rs17493370	1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs17493419	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs17493538	1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs17493573	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17493594	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17575960	0.82[CEU][hapmap]
rs17603796	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1864828	1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1864829	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864830	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2253519	0.82[EUR][1000 genomes]
rs3213851	0.81[ASN][1000 genomes]
rs34462852	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34533895	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34688430	0.81[ASN][1000 genomes]
rs34821677	0.81[ASN][1000 genomes]
rs35151237	0.81[EUR][1000 genomes]
rs35219064	0.96[EUR][1000 genomes]
rs35378647	0.82[ASN][1000 genomes]
rs35492507	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35581112	0.85[ASN][1000 genomes]
rs35679136	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35734673	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35869291	0.81[EUR][1000 genomes]
rs3731843	0.89[JPT][hapmap]
rs4268910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4536633	0.81[ASN][1000 genomes]
rs55948796	0.81[ASN][1000 genomes]
rs56208611	0.83[ASN][1000 genomes]
rs56217714	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6544169	0.82[EUR][1000 genomes]
rs6544170	0.81[JPT][hapmap]
rs6704829	0.83[ASN][1000 genomes]
rs6710118	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6722560	0.81[ASN][1000 genomes]
rs6731029	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6733848	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6736320	0.82[EUR][1000 genomes]
rs6745023	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6749343	0.88[EUR][1000 genomes]
rs6750764	0.81[ASN][1000 genomes]
rs68109027	0.82[ASN][1000 genomes]
rs72905846	0.82[ASN][1000 genomes]
rs72905865	0.95[ASN][1000 genomes]
rs72907903	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7573095	0.86[ASN][1000 genomes]
rs7574556	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs891705	0.89[JPT][hapmap]
rs919698	0.88[CEU][hapmap]
rs934394	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs934395	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
2	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
5	chr2:38779600-38812800	Weak transcription	Aorta	Aorta
6	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
7	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
8	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
11	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:38795200-38814800	Weak transcription	Gastric	stomach
14	chr2:38796400-38812800	Weak transcription	Small Intestine	intestine
15	chr2:38798000-38818000	Weak transcription	Stomach Mucosa	stomach
16	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
17	chr2:38798200-38812800	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:38798200-38812800	Weak transcription	Thymus	Thymus
19	chr2:38798200-38820600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:38798600-38816400	Weak transcription	Brain Germinal Matrix	brain
23	chr2:38798800-38817000	Weak transcription	Brain Anterior Caudate	brain
24	chr2:38798800-38822000	Weak transcription	NHEK	skin
25	chr2:38799600-38817200	Weak transcription	Brain Substantia Nigra	brain
26	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:38800000-38814000	Strong transcription	HSMM	muscle
28	chr2:38800000-38817800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:38800000-38818600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:38800600-38816600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:38802800-38819000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:38803600-38813000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr2:38803600-38813200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr2:38805200-38811800	Weak transcription	Fetal Brain Male	brain
35	chr2:38805200-38826400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:38806400-38814200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:38806800-38813000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:38807200-38819000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:38807800-38813000	Strong transcription	Fetal Lung	lung
40	chr2:38808000-38812600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:38808200-38824400	Weak transcription	Hela-S3	cervix
42	chr2:38808400-38820400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:38808800-38812000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:38808800-38812200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:38808800-38812400	Weak transcription	Adipose Nuclei	Adipose
46	chr2:38808800-38812800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:38808800-38812800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:38808800-38813400	Weak transcription	Primary T cells from cord blood	blood
49	chr2:38808800-38815200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:38808800-38815400	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links