Variant report

Variant	rs1497388
Chromosome Location	chr4:143339542-143339543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10519659	0.85[CHD][hapmap]
rs1155075	0.84[YRI][hapmap];0.89[AFR][1000 genomes]
rs11938760	0.83[JPT][hapmap];0.91[MEX][hapmap]
rs13133199	0.82[AMR][1000 genomes]
rs1391095	0.86[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap]
rs1391097	0.89[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1497386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17016027	0.89[GIH][hapmap];0.92[JPT][hapmap]
rs2029990	0.83[JPT][hapmap]
rs2130253	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2646095	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs2840094	0.89[AFR][1000 genomes]
rs3756125	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes]
rs3775707	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4626289	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6838117	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1497388	ZNF827	cis	parietal	SCAN
rs1497388	SCOC	cis	parietal	SCAN
rs1497388	LSM6	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143329000-143350000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:143330200-143344800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:143336000-143341000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:143336200-143340800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:143338000-143341200	Enhancers	Fetal Heart	heart
6	chr4:143338400-143340800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:143338400-143341000	Weak transcription	HSMM	muscle
8	chr4:143338600-143340400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:143338600-143341000	Weak transcription	HUVEC	blood vessel
10	chr4:143338600-143342000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr4:143338600-143344800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:143338600-143348800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:143338600-143366600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:143339000-143340000	Weak transcription	Left Ventricle	heart
15	chr4:143339000-143340200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:143339000-143341800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:143339000-143355400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:143339400-143341600	Weak transcription	HMEC	breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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