Variant report

Variant	rs1975820
Chromosome Location	chr11:93081815-93081816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1456238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1869914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2019814	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2259633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2446061	0.92[JPT][hapmap]
rs2605574	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2605580	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2605581	0.92[JPT][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs2605583	0.82[CEU][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap]
rs2608214	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2608215	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2658773	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2658775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2658776	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2658777	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap]
rs2658778	0.92[JPT][hapmap];0.82[YRI][hapmap]
rs2658782	0.90[JPT][hapmap]
rs2658791	0.81[EUR][1000 genomes]
rs2925355	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925362	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925938	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3019205	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3019206	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3019221	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019223	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3020073	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3020076	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3020083	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56091149	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72972357	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72972364	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv898180	chr11:93045561-93082053	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv468793	chr11:93068163-93129893	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1975820	CCDC67	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93078600-93082000	Weak transcription	K562	blood
2	chr11:93081200-93083400	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr11:93081400-93082000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr11:93081400-93082000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr11:93081600-93082000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr11:93081600-93082600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr11:93081600-93083400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr11:93081600-93083800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr11:93081800-93082000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr11:93081800-93082000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr11:93081800-93083400	Enhancers	H9 Cell Line	embryonic stem cell

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