Variant report

Variant	rs7663545
Chromosome Location	chr4:104179046-104179047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:104117492..104119427-chr4:104178040..104180048,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11728175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732717	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12498203	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12499479	0.84[EUR][1000 genomes]
rs12502466	0.83[EUR][1000 genomes]
rs12504679	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28420729	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4352478	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4698880	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4698886	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4698888	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4698891	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4699064	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699065	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699066	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55784701	0.83[EUR][1000 genomes]
rs58265700	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59776785	0.83[EUR][1000 genomes]
rs62329002	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62329005	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62329006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62338900	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62338902	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62338903	0.86[EUR][1000 genomes]
rs62338908	0.82[EUR][1000 genomes]
rs6816172	0.86[EUR][1000 genomes]
rs6819022	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819242	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6820979	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6822395	0.83[EUR][1000 genomes]
rs6838853	0.86[EUR][1000 genomes]
rs6844296	0.83[EUR][1000 genomes]
rs6844334	0.83[EUR][1000 genomes]
rs6847360	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72666831	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7676474	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7686331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
2	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830022	chr4:104087199-104257784	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv821637	chr4:104134839-104246167	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7663545	NHEDC1	cis	cerebellum	SCAN
rs7663545	TET2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104176600-104179800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:104177000-104179200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr4:104177200-104179400	Active TSS	HepG2	liver
4	chr4:104177200-104180000	Active TSS	K562	blood
5	chr4:104177600-104179400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:104177800-104179400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr4:104178800-104179800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:104178800-104180400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:104179000-104183000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links