Variant report

Variant	rs7684642
Chromosome Location	chr4:57727455-57727456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11721387	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11726410	0.91[ASN][1000 genomes]
rs11726443	0.91[ASN][1000 genomes]
rs11726548	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11727329	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11731657	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13123018	0.83[ASN][1000 genomes]
rs13125082	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13128671	0.83[ASN][1000 genomes]
rs13130600	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13130604	0.83[ASN][1000 genomes]
rs2412761	0.91[ASN][1000 genomes]
rs34308849	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34840470	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34937594	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35185186	0.83[ASN][1000 genomes]
rs35318869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413466	0.91[ASN][1000 genomes]
rs4443350	0.91[ASN][1000 genomes]
rs56143151	0.91[ASN][1000 genomes]
rs62308068	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62308099	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308100	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308107	1.00[ASN][1000 genomes]
rs62308153	0.91[ASN][1000 genomes]
rs66619445	0.83[ASN][1000 genomes]
rs6839166	0.91[ASN][1000 genomes]
rs7685053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9055	0.83[ASN][1000 genomes]
rs9760540	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7684642	RP11-738E22.3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57723400-57727600	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:57724600-57729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:57725000-57729400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:57725000-57729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:57725000-57729600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr4:57725200-57729800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:57727200-57727600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr4:57727200-57727600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr4:57727200-57727800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr4:57727200-57727800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr4:57727200-57727800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr4:57727200-57728000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:57727400-57727600	Enhancers	GM12878-XiMat	blood
14	chr4:57727400-57727800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:57727400-57727800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:57727400-57727800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:57727400-57728000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:57727400-57728000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links