Variant report

Variant	rs972491
Chromosome Location	chr2:213316573-213316574
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10201067	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs1026882	0.85[CEU][hapmap]
rs1283310	1.00[CHB][hapmap]
rs13419353	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs1384293	0.85[CEU][hapmap]
rs1384295	0.85[CEU][hapmap]
rs1905139	0.85[CEU][hapmap]
rs2054617	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2888093	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4106226	1.00[CHB][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs4673664	0.88[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs6435701	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6435705	0.88[ASN][1000 genomes]
rs6435707	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7556832	0.83[CEU][hapmap]
rs7565622	0.85[CEU][hapmap]
rs974968	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[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	nsv834527	chr2:213115966-213334308	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1004573	chr2:213186537-213365252	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv875811	chr2:213200920-213347104	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv432024	chr2:213314899-213446726	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs972491	LANCL1	cis	parietal	SCAN
rs972491	PIKFYVE	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213312200-213320400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:213314000-213316600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:213314200-213316600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:213315800-213316600	Enhancers	Fetal Heart	heart
5	chr2:213315800-213317200	Enhancers	NHEK	skin
6	chr2:213315800-213317400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:213316200-213316600	Active TSS	A549	lung
8	chr2:213316200-213317000	Enhancers	Fetal Kidney	kidney
9	chr2:213316400-213316600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr2:213316400-213316600	Flanking Active TSS	HepG2	liver
11	chr2:213316400-213316800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:213316400-213316800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:213316400-213316800	Enhancers	Brain Hippocampus Middle	brain
14	chr2:213316400-213317000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr2:213316400-213317000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:213316400-213317000	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:213316400-213317000	Enhancers	Brain Substantia Nigra	brain
18	chr2:213316400-213317000	Enhancers	HMEC	breast
19	chr2:213316400-213317000	Enhancers	HSMMtube	muscle
20	chr2:213316400-213317200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:213316400-213317200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:213316400-213317200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:213316400-213317200	Enhancers	NHDF-Ad	bronchial

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