Variant report

Variant	rs7707841
Chromosome Location	chr5:147492108-147492109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10038561	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10038991	0.85[EUR][1000 genomes]
rs10059850	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13185274	0.85[ASN][1000 genomes]
rs1862439	0.84[EUR][1000 genomes]
rs1862445	0.83[EUR][1000 genomes]
rs1862446	0.83[EUR][1000 genomes]
rs2287772	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777140	0.84[EUR][1000 genomes]
rs3777143	0.85[EUR][1000 genomes]
rs3815735	0.83[EUR][1000 genomes]
rs3815737	0.82[EUR][1000 genomes]
rs4333302	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4472254	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4510567	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4529181	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705223	0.82[EUR][1000 genomes]
rs6580518	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6580519	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580520	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6864564	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6864920	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6889688	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6894384	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6896914	0.85[EUR][1000 genomes]
rs988885	0.85[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	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7707841	SPINK5	cis	Thyroid	GTEx
rs7707841	SPINK5	cis	Adipose Subcutaneous	GTEx
rs7707841	SPINK5	cis	Heart Left Ventricle	GTEx
rs7707841	SPINK5	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147470400-147518400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr5:147470600-147508400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:147470600-147509000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:147471600-147514800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:147472000-147505000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:147472600-147497200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:147474200-147513400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:147479000-147500600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:147479200-147494200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:147480800-147498200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:147481400-147513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:147481600-147505000	Weak transcription	Esophagus	oesophagus
13	chr5:147482200-147509000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:147486800-147515000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:147487400-147505000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:147487800-147525800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:147489800-147493800	Weak transcription	Hela-S3	cervix
18	chr5:147490000-147493600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:147490800-147492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:147491600-147492400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:147491800-147493600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:147491800-147494000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:147491800-147495000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links