Variant report

Variant	rs3843695
Chromosome Location	chr15:60003668-60003669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59990164..59992393-chr15:60002065..60004419,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11629681	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11634157	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11637359	0.83[CHD][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs11854063	0.80[MEX][hapmap]
rs12438078	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs12439645	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12439658	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12439707	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12440020	0.83[EUR][1000 genomes]
rs12442896	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12443242	0.83[EUR][1000 genomes]
rs12443297	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902582	0.80[MEX][hapmap]
rs12904505	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12910451	0.83[EUR][1000 genomes]
rs17191002	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17236867	0.84[EUR][1000 genomes]
rs1871499	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs1871500	0.80[MEX][hapmap]
rs1871503	0.80[AMR][1000 genomes]
rs1871504	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1979423	0.82[ASN][1000 genomes]
rs2101019	0.83[CHD][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs2306357	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2306358	0.83[EUR][1000 genomes]
rs2307273	0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap]
rs28478168	0.82[ASN][1000 genomes]
rs2899649	0.89[JPT][hapmap]
rs3087328	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs3825870	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs3848119	0.83[EUR][1000 genomes]
rs3912205	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3912206	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3936513	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4270113	0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs4775200	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56141740	0.83[EUR][1000 genomes]
rs6151440	0.83[EUR][1000 genomes]
rs6151441	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151442	0.83[EUR][1000 genomes]
rs6151444	0.83[EUR][1000 genomes]
rs6151445	0.83[EUR][1000 genomes]
rs6151446	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6151447	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6151448	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6151449	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6151450	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs6151451	0.83[EUR][1000 genomes]
rs6151483	0.83[ASW][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs6151487	0.80[AMR][1000 genomes]
rs6151510	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs6151525	0.90[JPT][hapmap]
rs6151551	0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap]
rs6151553	0.86[JPT][hapmap]
rs6151561	0.89[JPT][hapmap]
rs6151568	0.80[MEX][hapmap]
rs6151586	0.80[MEX][hapmap]
rs6151588	0.80[MEX][hapmap]
rs6151589	0.80[MEX][hapmap]
rs6494138	0.83[EUR][1000 genomes]
rs6494139	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6494140	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7162645	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7173534	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173827	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7178211	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs728037	0.81[EUR][1000 genomes]
rs728038	0.81[EUR][1000 genomes]
rs754642	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs754643	0.83[EUR][1000 genomes]
rs755605	0.83[EUR][1000 genomes]
rs7882	0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs8026404	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8041394	0.80[MEX][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3843695	GTF2A2	cis	parietal	SCAN
rs3843695	NARG2	cis	parietal	SCAN
rs3843695	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:60002200-60004800	Enhancers	Fetal Lung	lung
2	chr15:60003200-60003800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:60003400-60004000	Enhancers	Brain Germinal Matrix	brain
4	chr15:60003400-60004200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:60003400-60004600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr15:60003600-60004600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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