Variant report

Variant	rs1868881
Chromosome Location	chr11:57901176-57901177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57899133..57901340-chr11:57902195..57904014,2	K562	blood:
2	chr11:57893156..57895554-chr11:57899477..57901378,2	K562	blood:
3	chr11:57900929..57901568-chr9:108114414..108115317,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1031360	0.88[CEU][hapmap]
rs10896701	0.92[CEU][hapmap]
rs11229264	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11600060	0.84[CEU][hapmap]
rs11601841	0.84[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs11604473	0.84[CEU][hapmap]
rs11604630	0.84[CEU][hapmap]
rs12283722	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12788387	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs12805812	0.84[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs1376489	0.94[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1447166	0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs17152364	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs17152376	0.84[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap]
rs1814059	0.84[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2245676	0.88[CEU][hapmap]
rs2441970	0.87[CEU][hapmap]
rs2443441	0.88[CEU][hapmap]
rs2514176	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs36104388	0.81[EUR][1000 genomes]
rs3853676	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs3862656	0.81[EUR][1000 genomes]
rs4509781	0.81[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs4939180	0.88[CEU][hapmap]
rs56298140	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61902775	0.81[EUR][1000 genomes]
rs61902797	0.81[EUR][1000 genomes]
rs61902798	0.82[EUR][1000 genomes]
rs61902799	0.82[EUR][1000 genomes]
rs7113760	0.81[CEU][hapmap]
rs7120102	0.80[CEU][hapmap]
rs7120442	0.84[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs7130381	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7930102	0.94[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7934149	0.82[EUR][1000 genomes]
rs7934184	0.84[CEU][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7935428	0.84[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap]
rs7938062	0.84[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7945154	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7948507	0.82[EUR][1000 genomes]
rs7949119	0.82[EUR][1000 genomes]
rs7949558	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs895660	0.92[CEU][hapmap]
rs930703	0.84[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832165	chr11:57806024-58009076	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv832166	chr11:57852031-58006189	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1868881	OR5M1	cis	cerebellum	SCAN
rs1868881	OR4D6	cis	cerebellum	SCAN
rs1868881	DDB1	cis	cerebellum	SCAN
rs1868881	UBE2L6	cis	parietal	SCAN
rs1868881	SYT7	cis	cerebellum	SCAN
rs1868881	TIMM10	cis	multi-tissue	Pritchard
rs1868881	PRG3	cis	parietal	SCAN
rs1868881	MS4A2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57900000-57901800	Enhancers	NHEK	skin
2	chr11:57900200-57901600	Enhancers	Fetal Intestine Large	intestine
3	chr11:57900400-57901600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:57900800-57901200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:57901000-57901400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr11:57901000-57901400	Enhancers	HepG2	liver
7	chr11:57901000-57901600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr11:57901000-57901600	Enhancers	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links