Variant report

Variant	rs13057878
Chromosome Location	chr22:30563720-30563721
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30562803..30564528-chr22:30605474..30607789,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1122239	0.83[ASN][1000 genomes]
rs1160671	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12233358	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12483946	0.92[CHB][hapmap]
rs12484420	0.84[AFR][1000 genomes]
rs12484547	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12484740	1.00[CEU][hapmap]
rs12484983	0.81[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs13053765	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13054837	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13055998	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13056332	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056990	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13057204	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13057580	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13057733	0.82[ASN][1000 genomes]
rs1476514	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16988123	0.84[AFR][1000 genomes]
rs16988145	0.84[AFR][1000 genomes]
rs2010916	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2012308	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2106430	0.95[EUR][1000 genomes]
rs2106722	0.95[ASN][1000 genomes]
rs2214047	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412977	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412979	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34391152	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34420020	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34474867	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34545612	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35067150	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35539897	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35710453	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36018230	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3788422	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4820825	0.84[AFR][1000 genomes]
rs4820829	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4823067	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823071	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4823080	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4823081	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4823082	0.95[EUR][1000 genomes]
rs5752997	0.84[AFR][1000 genomes]
rs5753002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753007	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753013	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753015	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753019	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753020	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753022	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753027	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753028	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753029	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753030	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753046	0.95[EUR][1000 genomes]
rs5763637	0.84[AFR][1000 genomes]
rs5763648	0.84[AFR][1000 genomes]
rs5763681	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs5763687	0.84[AFR][1000 genomes]
rs5763695	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs5763701	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs5763734	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763742	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763748	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763749	0.85[ASN][1000 genomes]
rs5763750	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763758	0.91[ASN][1000 genomes]
rs5763759	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763763	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763766	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763769	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763774	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763782	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763787	0.91[ASN][1000 genomes]
rs5763788	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763801	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763805	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763810	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763825	0.97[ASN][1000 genomes]
rs5763852	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763854	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763861	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763872	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6006393	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs718773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7286304	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7286681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7288576	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs739616	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs757026	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs766011	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8138404	0.84[AFR][1000 genomes]
rs8142101	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs916807	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs975704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv527188	chr22:30529741-30581722	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13057878	LGALS8	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30558200-30563800	Weak transcription	Dnd41	blood
2	chr22:30558400-30564400	Weak transcription	Fetal Thymus	thymus
3	chr22:30563000-30563800	Enhancers	Thymus	Thymus
4	chr22:30563000-30564600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr22:30563000-30567000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr22:30563200-30566600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr22:30563400-30566400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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