Variant report

Variant	rs11742783
Chromosome Location	chr5:128114425-128114426
allele	C/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:19)

rs_ID	r²[population]
rs10042834	0.82[EUR][1000 genomes]
rs10075245	0.82[EUR][1000 genomes]
rs1012263	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11741074	0.82[EUR][1000 genomes]
rs12054810	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12522121	0.82[EUR][1000 genomes]
rs12719381	0.82[EUR][1000 genomes]
rs13156561	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13169119	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13181669	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13186067	0.81[EUR][1000 genomes]
rs13190353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1422444	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1422447	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35111151	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4836401	0.81[EUR][1000 genomes]
rs4836403	0.82[EUR][1000 genomes]
rs4836404	0.82[EUR][1000 genomes]
rs4836406	0.81[EUR][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	nsv1023405	chr5:127955360-128190069	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv882836	chr5:127999225-128136519	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	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
rs11742783	SLC27A6	cis	parietal	SCAN
rs11742783	CCNI2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128112600-128114600	Enhancers	HUVEC	blood vessel
2	chr5:128112600-128114800	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr5:128112600-128115400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:128112800-128114800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:128112800-128115000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr5:128112800-128115400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr5:128112800-128115400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:128113600-128114600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:128113600-128114800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr5:128113600-128115000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:128113800-128114600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:128114000-128115000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:128114200-128114600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr5:128114200-128114600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:128114200-128114600	Flanking Active TSS	NH-A	brain
16	chr5:128114200-128114800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:128114200-128117800	Weak transcription	Fetal Stomach	stomach
18	chr5:128114400-128115000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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