Variant report

Variant	rs6741751
Chromosome Location	chr2:234827661-234827662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234761504..234764477-chr2:234824983..234827662,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123485	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1004478	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10490010	0.93[CEU][hapmap]
rs10803665	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10803666	0.93[CEU][hapmap]
rs10929317	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11562941	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11562954	0.93[CEU][hapmap]
rs11562979	0.87[ASN][1000 genomes]
rs11563228	0.90[ASN][1000 genomes]
rs12470426	0.82[CHB][hapmap]
rs12472151	0.82[CHB][hapmap]
rs12473889	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs12988953	0.96[EUR][1000 genomes]
rs13020968	0.82[CHB][hapmap]
rs13028228	0.93[CEU][hapmap]
rs13390819	0.90[ASN][1000 genomes]
rs13398248	0.83[ASN][1000 genomes]
rs13403318	0.90[ASN][1000 genomes]
rs13406453	0.90[ASN][1000 genomes]
rs13406457	0.87[ASN][1000 genomes]
rs13410024	0.90[ASN][1000 genomes]
rs13410032	0.90[ASN][1000 genomes]
rs17862907	0.90[ASN][1000 genomes]
rs17862920	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17862921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17863825	0.90[ASN][1000 genomes]
rs17863826	0.90[ASN][1000 genomes]
rs17863838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17863841	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs17863842	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs17864729	0.90[ASN][1000 genomes]
rs17864738	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17864741	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17868368	0.90[ASN][1000 genomes]
rs17868369	0.83[ASN][1000 genomes]
rs186159	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs188492	0.93[ASN][1000 genomes]
rs213541	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs213543	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs213544	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs213550	0.93[ASN][1000 genomes]
rs2173746	0.90[ASN][1000 genomes]
rs2173747	0.90[ASN][1000 genomes]
rs2530796	0.90[ASN][1000 genomes]
rs2650888	0.90[ASN][1000 genomes]
rs35168608	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs494812	0.90[ASN][1000 genomes]
rs498680	0.90[ASN][1000 genomes]
rs498696	0.90[ASN][1000 genomes]
rs498786	0.83[ASN][1000 genomes]
rs498790	0.83[ASN][1000 genomes]
rs499703	0.90[ASN][1000 genomes]
rs501650	0.90[ASN][1000 genomes]
rs502321	0.90[ASN][1000 genomes]
rs506632	0.90[ASN][1000 genomes]
rs511387	0.93[ASN][1000 genomes]
rs531771	0.90[ASN][1000 genomes]
rs566985	0.93[ASN][1000 genomes]
rs568906	0.93[ASN][1000 genomes]
rs570800	0.93[ASN][1000 genomes]
rs575194	0.90[ASN][1000 genomes]
rs577734	0.90[ASN][1000 genomes]
rs577782	0.90[ASN][1000 genomes]
rs577820	0.90[ASN][1000 genomes]
rs579327	0.90[ASN][1000 genomes]
rs581377	0.90[ASN][1000 genomes]
rs596509	0.90[ASN][1000 genomes]
rs598759	0.83[ASN][1000 genomes]
rs598760	0.83[ASN][1000 genomes]
rs611131	0.90[ASN][1000 genomes]
rs611169	0.90[ASN][1000 genomes]
rs611563	0.90[ASN][1000 genomes]
rs622954	0.87[ASN][1000 genomes]
rs625151	0.90[ASN][1000 genomes]
rs628138	0.90[ASN][1000 genomes]
rs657658	0.90[ASN][1000 genomes]
rs658054	0.90[ASN][1000 genomes]
rs658607	0.90[ASN][1000 genomes]
rs6717978	0.98[EUR][1000 genomes]
rs6717992	0.98[EUR][1000 genomes]
rs672831	0.90[ASN][1000 genomes]
rs686003	0.83[ASN][1000 genomes]
rs686007	0.83[ASN][1000 genomes]
rs688677	0.90[ASN][1000 genomes]
rs7558436	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs7562952	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs7562971	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs7577262	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9646718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

Variant related diseases (count:4)

Disease	PMID	Source
Migraine - clinic-based	23793025	GWAS catalog
Migraine with aura	23793025	GWAS catalog
Migraine	23793025	GWAS catalog
Migraine without aura	23793025	GWAS catalog

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234826200-234830000	Weak transcription	Brain Germinal Matrix	brain
2	chr2:234827600-234827800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:234827600-234829800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:234827600-234834000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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