Variant report

Variant	rs7577894
Chromosome Location	chr2:56008904-56008905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:56008821..56010807-chr2:56013593..56015981,2	MCF-7	breast:
2	chr2:56006149..56008907-chr2:56021297..56024096,2	MCF-7	breast:
3	chr2:56006332..56008999-chr2:56065171..56067853,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11125600	0.85[ASN][1000 genomes]
rs11676678	0.89[ASN][1000 genomes]
rs11684982	0.89[ASN][1000 genomes]
rs11693187	0.85[ASN][1000 genomes]
rs11694759	0.89[ASN][1000 genomes]
rs11694790	0.89[ASN][1000 genomes]
rs11887339	0.89[ASN][1000 genomes]
rs12614845	0.89[ASN][1000 genomes]
rs13404193	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1367228	0.82[CHB][hapmap]
rs1430191	0.82[CHB][hapmap]
rs1430198	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1430199	0.89[ASN][1000 genomes]
rs1430200	0.89[ASN][1000 genomes]
rs1465624	0.89[ASN][1000 genomes]
rs1465625	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1961386	0.82[AMR][1000 genomes]
rs3791676	0.82[CHB][hapmap]
rs4233963	0.83[ASN][1000 genomes]
rs4672069	0.89[ASN][1000 genomes]
rs6714513	0.82[CHB][hapmap]
rs6723918	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6742316	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6747885	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6753814	0.82[CHB][hapmap]
rs6761334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7426380	0.82[CHB][hapmap]
rs7560508	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9309269	0.89[ASN][1000 genomes]
rs9309270	0.94[ASN][1000 genomes]
rs934274	0.92[ASN][1000 genomes]
rs934275	0.92[ASN][1000 genomes]
rs934276	0.89[ASN][1000 genomes]
rs934277	0.89[ASN][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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv999962	chr2:55976574-56011517	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv997683	chr2:55976574-56013875	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv431080	chr2:55988293-56011517	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Amyotrophic lateral sclerosis	19451621	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7577894	EFEMP1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55989400-56015000	Weak transcription	Aorta	Aorta
2	chr2:56006200-56010200	Enhancers	Hela-S3	cervix
3	chr2:56006400-56009000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:56007400-56009000	Enhancers	HUVEC	blood vessel
5	chr2:56007600-56009400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:56008000-56009000	Enhancers	NHEK	skin
7	chr2:56008000-56009600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:56008200-56009200	Enhancers	A549	lung
9	chr2:56008200-56009400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:56008200-56009600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:56008200-56010000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:56008200-56010000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:56008200-56010200	Enhancers	HMEC	breast
14	chr2:56008200-56010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:56008800-56010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:56008800-56010400	Weak transcription	HSMM	muscle

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