Variant report

Variant	rs3912428
Chromosome Location	chr2:54432222-54432223
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	chr2:54430392..54431993-chr2:54432039..54434857,2	MCF-7	breast:
2	chr2:54431810..54434797-chr2:54434888..54436507,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10188489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10439478	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10865281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11125526	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11125528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11884867	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11886559	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11893929	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11894205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11899551	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11902901	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12612860	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616744	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12616857	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13410397	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13412139	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13417493	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1385273	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1399513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1484692	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17045583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045585	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045588	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17045654	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17045658	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17045688	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17045704	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1986036	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2010461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35126790	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3915270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55743218	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56042969	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56755567	0.93[EUR][1000 genomes]
rs58107053	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62138037	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62139188	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6717823	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6723912	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6732970	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72802630	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72802650	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7567646	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7602930	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7607356	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv874148	chr2:54344325-54432222	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv874149	chr2:54358517-54432222	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1009828	chr2:54393122-54488721	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	nsv525086	chr2:54432222-54459211	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3912428	EFEMP1	cis	parietal	SCAN
rs3912428	RTN4	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54380600-54434400	Weak transcription	Ovary	ovary
2	chr2:54387800-54457400	Weak transcription	Aorta	Aorta
3	chr2:54388400-54435000	Weak transcription	Brain Angular Gyrus	brain
4	chr2:54404200-54433600	Weak transcription	Brain Anterior Caudate	brain
5	chr2:54412600-54435000	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:54414200-54434600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:54415200-54432400	Weak transcription	Primary B cells from cord blood	blood
8	chr2:54415200-54434200	Weak transcription	Primary T cells from cord blood	blood
9	chr2:54415200-54434400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:54415200-54434600	Weak transcription	HSMMtube	muscle
11	chr2:54415400-54434400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:54416200-54451400	Weak transcription	Left Ventricle	heart
13	chr2:54423800-54434400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:54427600-54434400	Weak transcription	NHLF	lung
15	chr2:54431400-54435200	Enhancers	HepG2	liver
16	chr2:54431800-54432600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr2:54431800-54432600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:54432000-54433800	Enhancers	Fetal Lung	lung
19	chr2:54432000-54434200	Weak transcription	Adipose Nuclei	Adipose
20	chr2:54432000-54434600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:54432200-54432800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:54432200-54434200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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