Variant report

Variant	rs6539171
Chromosome Location	chr12:105302961-105302962
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	chr12:105302265..105304511-chr12:105355863..105357764,2	K562	blood:
2	chr12:105297810..105300145-chr12:105300569..105303265,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1002803	0.83[CHB][hapmap]
rs10507184	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs10746008	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778355	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10778358	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861294	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10861296	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112253	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1155994	0.82[ASN][1000 genomes]
rs11610388	0.81[ASN][1000 genomes]
rs1389612	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1565813	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2248012	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2248986	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249454	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2264892	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453156	0.89[CHB][hapmap]
rs2453166	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2463018	0.88[CHB][hapmap]
rs2468092	0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2468099	0.81[ASN][1000 genomes]
rs2468100	0.81[ASN][1000 genomes]
rs2468105	0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2468337	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468340	0.81[ASN][1000 genomes]
rs2730291	0.83[CHB][hapmap]
rs4334113	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4388976	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4393404	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964310	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6539170	0.88[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7135015	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138686	0.86[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7309240	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73193606	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7967503	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7968763	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7980681	0.81[ASN][1000 genomes]
rs9668618	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs996294	0.81[CEU][hapmap]

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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6539171	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105278600-105313800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:105284600-105309000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:105290800-105331600	Weak transcription	Gastric	stomach
4	chr12:105293400-105310000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:105293600-105303800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:105293600-105321600	Weak transcription	A549	lung
7	chr12:105297400-105306600	Weak transcription	Ovary	ovary
8	chr12:105297400-105323600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:105297600-105323400	Weak transcription	Aorta	Aorta
10	chr12:105297800-105313000	Weak transcription	Fetal Stomach	stomach
11	chr12:105298200-105303200	Weak transcription	Adipose Nuclei	Adipose
12	chr12:105298200-105303800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:105298200-105314600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:105300000-105303800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:105300400-105323200	Weak transcription	Pancreas	Pancrea
16	chr12:105301400-105303200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:105302600-105304600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:105302800-105303400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:105302800-105303400	Strong transcription	Liver	Liver
20	chr12:105302800-105304800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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