Variant report

Variant	rs12085288
Chromosome Location	chr1:212075555-212075556
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	chr1:212074801..212076576-chr1:212084701..212087247,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10863929	0.89[ASN][1000 genomes]
rs11119813	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11487823	0.83[ASN][1000 genomes]
rs1157168	0.85[JPT][hapmap]
rs12059988	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12076991	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12077561	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12084756	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12085235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090490	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12095938	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2788123	0.86[JPT][hapmap]
rs28768080	0.84[ASN][1000 genomes]
rs28800280	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28862981	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2970578	1.00[JPT][hapmap]
rs3738197	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs3862952	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4447046	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4537651	0.84[ASN][1000 genomes]
rs4562685	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4623773	0.89[ASN][1000 genomes]
rs56132364	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61828491	0.83[ASN][1000 genomes]
rs61828510	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6540709	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6662067	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6664082	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6666948	1.00[JPT][hapmap]
rs6678582	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6684049	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6704043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7518896	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7524009	0.84[JPT][hapmap]
rs7534335	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs7547097	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762218	chr1:212046447-212087682	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12085288	INTS7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212074400-212078400	Enhancers	Fetal Intestine Small	intestine
2	chr1:212074400-212078800	Enhancers	Fetal Intestine Large	intestine
3	chr1:212074600-212076200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:212074600-212077200	ZNF genes & repeats	GM12878-XiMat	blood
5	chr1:212074800-212076200	Enhancers	Esophagus	oesophagus
6	chr1:212075000-212075600	Weak transcription	Colonic Mucosa	Colon
7	chr1:212075200-212075800	Enhancers	Rectal Mucosa Donor 29	rectum

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