Variant report

Variant	rs10916277
Chromosome Location	chr1:228386374-228386375
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	chr1:228372145..228374632-chr1:228384482..228386593,2	K562	blood:
2	chr1:228352906..228354898-chr1:228384251..228386544,2	K562	blood:

Variant related genes	Relation type
ENSG00000181873	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10753445	0.82[EUR][1000 genomes]
rs12084338	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12097591	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12130630	0.91[EUR][1000 genomes]
rs12134624	0.89[EUR][1000 genomes]
rs1411911	0.85[EUR][1000 genomes]
rs1557026	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17623766	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17640616	0.86[EUR][1000 genomes]
rs2185544	0.82[EUR][1000 genomes]
rs2298014	0.90[EUR][1000 genomes]
rs2313600	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653907	0.89[EUR][1000 genomes]
rs4653917	0.92[EUR][1000 genomes]
rs4653919	0.93[EUR][1000 genomes]
rs4653920	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653921	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55658545	0.86[EUR][1000 genomes]
rs55873533	0.89[EUR][1000 genomes]
rs61825279	0.82[EUR][1000 genomes]
rs6426492	0.81[EUR][1000 genomes]
rs6657968	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6661539	0.88[EUR][1000 genomes]
rs6673893	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6682260	0.91[EUR][1000 genomes]
rs72757811	0.91[EUR][1000 genomes]
rs72757812	0.91[EUR][1000 genomes]
rs72757824	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72757827	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72757829	0.89[EUR][1000 genomes]
rs7532141	0.84[EUR][1000 genomes]
rs7532924	0.80[EUR][1000 genomes]
rs7539762	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
11	esv1808523	chr1:228359177-228400358	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10916277	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs10916277	OBSCN	cis	Esophagus Mucosa	GTEx
rs10916277	IBA57	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228363400-228386400	Weak transcription	Brain Angular Gyrus	brain
2	chr1:228364400-228386600	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:228364400-228388600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:228364600-228386600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:228365200-228386600	Weak transcription	Thymus	Thymus
6	chr1:228365200-228387800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:228366000-228386400	Weak transcription	Primary B cells from cord blood	blood
8	chr1:228366800-228386600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:228366800-228393400	Weak transcription	Right Ventricle	heart
10	chr1:228371200-228386400	Weak transcription	Primary T cells from cord blood	blood
11	chr1:228373800-228394000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:228380400-228386400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:228381400-228386400	Weak transcription	Fetal Heart	heart
14	chr1:228382600-228393000	Weak transcription	Colonic Mucosa	Colon
15	chr1:228383200-228386400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:228383200-228394600	Weak transcription	Fetal Brain Male	brain
17	chr1:228385600-228386400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:228385600-228386600	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:228385600-228387800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:228385600-228392800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:228385600-228393400	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links