Variant report

Variant	rs7700649
Chromosome Location	chr5:179121263-179121264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10066644	0.90[ASN][1000 genomes]
rs11249653	0.85[ASN][1000 genomes]
rs11249654	0.87[ASN][1000 genomes]
rs11249658	0.96[YRI][hapmap]
rs11738962	0.81[CEU][hapmap]
rs11739941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11747219	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188590	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13159123	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13180726	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13361866	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17079630	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700839	0.81[CEU][hapmap]
rs4701197	0.81[CEU][hapmap]
rs62404341	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6627	0.81[CEU][hapmap]
rs6879613	0.81[CEU][hapmap]
rs7566	0.81[CEU][hapmap]
rs7723450	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
5	nsv969028	chr5:179117224-179123617	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7700649	PRR7	cis	cerebellum	SCAN
rs7700649	CANX	cis	parietal	SCAN
rs7700649	HRH2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179106600-179124200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:179106600-179124800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:179106800-179123000	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:179107400-179121400	Weak transcription	Primary B cells from cord blood	blood
5	chr5:179107600-179123200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:179107600-179123200	Weak transcription	Fetal Thymus	thymus
7	chr5:179107600-179123400	Weak transcription	Fetal Intestine Small	intestine
8	chr5:179108400-179123000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:179108600-179123600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:179114000-179123000	Weak transcription	HepG2	liver
11	chr5:179118400-179125000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:179120800-179122000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:179120800-179123800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:179121200-179121400	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr5:179121200-179122000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr5:179121200-179122800	Enhancers	Primary monocytes fromperipheralblood	blood

Quick Search:

Input of quick search could be:

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

what's new

Quick links