Variant report

Variant	rs6856593
Chromosome Location	chr4:104177699-104177700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1022348	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10516502	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097804	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11734165	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11943325	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1607095	0.82[EUR][1000 genomes]
rs17033498	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2085978	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2126471	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2169511	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2623060	0.81[CEU][hapmap]
rs2866642	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2866646	0.96[EUR][1000 genomes]
rs28837409	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4456958	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4698887	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4698890	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699062	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533056	0.88[CEU][hapmap]
rs6533078	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533079	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6822379	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6849319	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6850461	0.88[CEU][hapmap]
rs7657390	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7672802	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7676772	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7678717	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7679365	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs970156	0.85[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6856593	BDH2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 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	chr4:104177000-104177800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr4:104177000-104177800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:104177000-104178000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr4:104177000-104178800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr4:104177000-104178800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr4:104177000-104179200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:104177200-104178800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:104177200-104178800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr4:104177200-104179400	Active TSS	HepG2	liver
11	chr4:104177200-104180000	Active TSS	K562	blood
12	chr4:104177400-104178200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr4:104177600-104178000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr4:104177600-104179400	Active TSS	iPS-20b Cell Line	embryonic stem cell

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