Variant report

Variant	rs17680523
Chromosome Location	chr7:102936821-102936822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:102936427..102940589-chr7:102983649..102988902,7	K562	blood:
2	chr7:102936363..102940498-chr7:102983696..102986201,5	K562	blood:
3	chr7:102788341..102791545-chr7:102935934..102939308,4	K562	blood:
4	chr7:102936543..102939393-chr7:103085608..103089565,4	MCF-7	breast:
5	chr7:102935903..102938136-chr7:102983489..102985608,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105821	Chromatin interaction
ENSG00000161057	Chromatin interaction
ENSG00000234715	Chromatin interaction
ENSG00000161048	Chromatin interaction
ENSG00000170615	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10245155	0.93[ASN][1000 genomes]
rs10257369	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs10266523	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10486853	0.82[JPT][hapmap]
rs11978339	1.00[JPT][hapmap]
rs17136078	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs17136083	0.82[JPT][hapmap]
rs17136728	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs17606134	0.92[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs17837510	0.82[JPT][hapmap]
rs1861731	0.84[GIH][hapmap];0.82[JPT][hapmap]
rs1968201	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2193420	0.82[JPT][hapmap]
rs2878	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3087615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35399723	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4266582	0.88[GIH][hapmap]
rs4593456	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs4727563	0.91[GIH][hapmap];0.82[JPT][hapmap]
rs4727566	0.82[JPT][hapmap]
rs4727568	0.88[GIH][hapmap]
rs4729887	0.87[GIH][hapmap];0.82[JPT][hapmap]
rs4729891	0.82[JPT][hapmap]
rs4729896	0.82[JPT][hapmap]
rs4729911	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5025411	0.92[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs62482370	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62482394	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62482396	0.93[ASN][1000 genomes]
rs62482397	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62482398	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62482399	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62482403	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62482404	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482405	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62482406	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6971734	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs73175837	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73175852	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7455141	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs7777392	1.00[JPT][hapmap]
rs7804020	0.92[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv831084	chr7:102778908-102964970	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17680523	RP11-401L13.5	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102931800-102937400	Weak transcription	Fetal Brain Male	brain
2	chr7:102932800-102937400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:102933200-102937400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:102933600-102937200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:102933600-102937400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:102935000-102937200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:102936800-102937400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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