Variant report

Variant	rs6665186
Chromosome Location	chr1:185327527-185327528
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	chr1:185284808..185287790-chr1:185326640..185329248,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273004	Chromatin interaction
ENSG00000116679	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10157232	0.98[ASN][1000 genomes]
rs10157996	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs10158623	0.98[ASN][1000 genomes]
rs10737258	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10752948	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911706	0.84[EUR][1000 genomes]
rs10911711	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12044943	0.86[ASN][1000 genomes]
rs2207517	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2207518	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207519	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2295212	0.84[EUR][1000 genomes]
rs4651253	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6424975	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6424976	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs6656019	0.86[ASN][1000 genomes]
rs6659669	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6679327	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6682074	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66845254	0.98[ASN][1000 genomes]
rs6687774	0.82[CHD][hapmap]
rs6689206	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7512337	0.98[ASN][1000 genomes]
rs7519628	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7531487	0.86[ASN][1000 genomes]
rs7545878	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7548599	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988622	0.83[EUR][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	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	esv2756872	chr1:185293197-185345771	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2758981	chr1:185293197-185345771	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1008247	chr1:185321360-185345771	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6665186	LHX4	cis	parietal	SCAN
rs6665186	ARPC5	cis	cerebellum	SCAN
rs6665186	TOR1AIP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185313800-185327800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:185317600-185329400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:185319600-185330200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:185319600-185335600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:185325400-185328000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:185325400-185336400	Weak transcription	Right Atrium	heart
7	chr1:185326400-185329800	Weak transcription	HUVEC	blood vessel
8	chr1:185327400-185328200	ZNF genes & repeats	Fetal Intestine Small	intestine

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