Variant report

Variant	rs228180
Chromosome Location	chr6:38301169-38301170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1033480	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947728	0.83[EUR][1000 genomes]
rs10947729	0.83[EUR][1000 genomes]
rs1205108	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12201631	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12202804	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12208912	0.81[EUR][1000 genomes]
rs1931758	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2179532	0.83[EUR][1000 genomes]
rs2179533	0.83[EUR][1000 genomes]
rs228179	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs228186	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228188	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395698	0.83[EUR][1000 genomes]
rs2395699	0.83[EUR][1000 genomes]
rs4714147	0.91[ASN][1000 genomes]
rs4714148	0.91[ASN][1000 genomes]
rs7763775	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871183	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9349072	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38275400-38301200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:38278000-38310600	Weak transcription	Gastric	stomach
3	chr6:38278400-38305400	Weak transcription	Pancreas	Pancrea
4	chr6:38282600-38301400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:38283000-38304000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:38284800-38301200	Weak transcription	Fetal Intestine Small	intestine
7	chr6:38285000-38327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:38287400-38301200	Weak transcription	Primary B cells from cord blood	blood
9	chr6:38287600-38301200	Weak transcription	Primary T cells from cord blood	blood
10	chr6:38288000-38305600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:38291000-38305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:38291400-38317600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:38298600-38303600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:38299200-38313400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:38299600-38303000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:38299800-38317800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:38300200-38304800	Weak transcription	Fetal Brain Female	brain
18	chr6:38301000-38301200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:38301000-38301200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:38301000-38302000	ZNF genes & repeats	Primary B cells from peripheral blood	blood

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