Variant report

Variant	rs17161316
Chromosome Location	chr5:107756154-107756155
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107716061..107717776-chr5:107755624..107757305,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145743	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10515386	0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11747049	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12654121	0.91[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12654703	1.00[EUR][1000 genomes]
rs12656256	0.91[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12656744	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12656817	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12657054	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12658221	1.00[EUR][1000 genomes]
rs12659121	0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12659135	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17161236	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17161254	0.91[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17161284	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs17161304	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1965392	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2063422	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2122159	1.00[EUR][1000 genomes]
rs2910790	0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs2966787	0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2966791	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2966801	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs4423983	1.00[EUR][1000 genomes]
rs4463170	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4593253	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4957754	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55875758	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57067664	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57732790	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60493671	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60785751	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72503488	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73781360	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73781369	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7720469	0.87[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]

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	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17161316	ATF7IP2	trans	brain	seeQTL
rs17161316	XBP1	trans	brain	seeQTL
rs17161316	HSPA6	trans	brain	seeQTL
rs17161316	ACBD3	trans	brain	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107754800-107756200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:107754800-107757200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr5:107755200-107756200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:107755200-107756200	Enhancers	Brain Germinal Matrix	brain
5	chr5:107755200-107756400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:107755600-107756600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:107756000-107756200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:107756000-107756200	Enhancers	Fetal Brain Female	brain

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