Variant report

Variant	rs1208681
Chromosome Location	chr10:38092975-38092976
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	chr10:38092192..38094710-chr10:38111605..38114587,2	K562	blood:
2	chr10:38092650..38094653-chr10:38146551..38148241,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236514	Chromatin interaction
ENSG00000198105	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1022698	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10764147	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10827835	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10827836	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11011343	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11011351	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11011407	0.84[AMR][1000 genomes]
rs1208592	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1208684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1208689	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1208708	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1208767	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12774732	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13503	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1735577	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1779017	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1814077	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs200903	0.90[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200910	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200924	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs200935	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs200936	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200937	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200939	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs200943	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2144849	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2180408	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2472150	0.83[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap]
rs2504130	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2749592	0.82[JPT][hapmap]
rs289638	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs289648	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs289649	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851078	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4934906	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4934907	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4934912	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4934916	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7069702	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7099777	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs719569	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9417256	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[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	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv982874	chr10:38092839-38111415	ZNF genes & repeats Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1208681	ZNF25	cis	parietal	SCAN
rs1208681	ZNF25	cis	cerebellum	SCAN
rs1208681	HSD17B7P2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38081200-38097200	Weak transcription	Aorta	Aorta
2	chr10:38085400-38100800	Weak transcription	Left Ventricle	heart
3	chr10:38087400-38094600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr10:38090000-38093200	Weak transcription	Brain Substantia Nigra	brain
5	chr10:38090400-38101000	Weak transcription	HepG2	liver
6	chr10:38090600-38093000	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:38090800-38102200	Weak transcription	Brain Angular Gyrus	brain
8	chr10:38091200-38094000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:38091400-38094000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:38091800-38102400	Weak transcription	Brain Anterior Caudate	brain
11	chr10:38092000-38093000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr10:38092200-38093000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr10:38092200-38093000	Strong transcription	Adipose Nuclei	Adipose
14	chr10:38092200-38093000	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr10:38092600-38093000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr10:38092600-38094200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr10:38092600-38105000	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links