Variant report

Variant	rs2867008
Chromosome Location	chr4:79084236-79084237
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10008931	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018454	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10023697	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10025769	0.92[EUR][1000 genomes]
rs10029115	0.92[EUR][1000 genomes]
rs10029734	0.94[EUR][1000 genomes]
rs10030639	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10033428	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10213063	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10213609	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10518194	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs10856998	0.83[EUR][1000 genomes]
rs11098038	0.84[EUR][1000 genomes]
rs13106100	0.86[EUR][1000 genomes]
rs13106755	0.86[EUR][1000 genomes]
rs13130161	0.86[EUR][1000 genomes]
rs13144972	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13150598	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17002930	0.86[EUR][1000 genomes]
rs1878438	0.84[EUR][1000 genomes]
rs1878439	0.84[EUR][1000 genomes]
rs28479828	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28583476	0.92[EUR][1000 genomes]
rs28635454	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2867006	0.92[EUR][1000 genomes]
rs28677913	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28707182	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28750761	0.90[EUR][1000 genomes]
rs28796316	0.92[EUR][1000 genomes]
rs28822779	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28854287	0.90[EUR][1000 genomes]
rs2903453	0.91[EUR][1000 genomes]
rs35060393	0.93[ASN][1000 genomes]
rs4156	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4345212	0.86[EUR][1000 genomes]
rs4388115	0.86[EUR][1000 genomes]
rs4410553	0.86[EUR][1000 genomes]
rs4423900	0.84[EUR][1000 genomes]
rs4443313	0.82[EUR][1000 genomes]
rs4561952	0.92[EUR][1000 genomes]
rs4583783	0.86[EUR][1000 genomes]
rs4610363	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4634250	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58969863	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6820400	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6822247	0.86[EUR][1000 genomes]
rs6825089	0.93[ASN][1000 genomes]
rs6842152	0.86[EUR][1000 genomes]
rs6847174	0.86[EUR][1000 genomes]
rs6856815	0.83[EUR][1000 genomes]
rs6857278	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6857527	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72654653	0.86[EUR][1000 genomes]
rs7437861	0.86[EUR][1000 genomes]
rs7441634	0.90[EUR][1000 genomes]
rs7666444	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7672583	0.84[EUR][1000 genomes]
rs7675794	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7684543	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7689960	0.85[EUR][1000 genomes]
rs7698326	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9307335	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9307336	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9307337	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9307338	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9307339	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9307340	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9307352	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9991356	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9993527	0.92[EUR][1000 genomes]
rs9994298	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9994422	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9995229	0.92[EUR][1000 genomes]
rs9998932	0.93[EUR][1000 genomes]
rs9999763	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv879502	chr4:79052851-79144309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv829977	chr4:79082318-79110300	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2867008	FRAS1	cis	parietal	SCAN
rs2867008	SCARB2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79071400-79096600	Weak transcription	Pancreas	Pancrea
2	chr4:79078200-79085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:79078200-79094200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:79078400-79095600	Weak transcription	Psoas Muscle	Psoas
5	chr4:79081600-79084400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr4:79082400-79085200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr4:79082400-79086600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr4:79083000-79084400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:79083400-79085000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:79083600-79086200	Enhancers	HepG2	liver
11	chr4:79083800-79093000	Weak transcription	Fetal Heart	heart
12	chr4:79084000-79085000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:79084000-79085200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:79084000-79086600	Weak transcription	Fetal Intestine Small	intestine
15	chr4:79084200-79085200	Weak transcription	Fetal Kidney	kidney
16	chr4:79084200-79086200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:79084200-79086400	Weak transcription	Fetal Intestine Large	intestine
18	chr4:79084200-79091400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:79084200-79091400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:79084200-79091800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:79084200-79093000	Weak transcription	H9 Cell Line	embryonic stem cell

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