Variant report

Variant	rs32979
Chromosome Location	chr5:14119775-14119776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14118650..14121967-chr5:14142611..14144967,3	MCF-7	breast:
2	chr5:14117892..14119794-chr5:14142984..14144807,2	MCF-7	breast:
3	chr5:14010998..14013297-chr5:14117921..14120425,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs153191	0.83[LWK][hapmap];0.80[MKK][hapmap];0.88[YRI][hapmap]
rs153192	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs163813	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs163814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs163826	1.00[TSI][hapmap]
rs180738	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs185203	0.85[TSI][hapmap]
rs250844	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs250847	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs26290	1.00[CEU][hapmap]
rs26292	1.00[CEU][hapmap]
rs27367	1.00[CEU][hapmap]
rs27632	1.00[CEU][hapmap]
rs27666	1.00[CEU][hapmap]
rs32976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs32977	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33028	1.00[CEU][hapmap]
rs33029	1.00[CEU][hapmap]
rs33030	1.00[CEU][hapmap]
rs343883	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs348113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs348114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs348116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40298	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];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432716	chr5:13779700-14184600	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv516415	chr5:13788886-14210897	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1019196	chr5:13790760-14187503	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	esv2830407	chr5:13793627-14172298	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv1020810	chr5:13798819-14160981	Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv1024836	chr5:13798819-14170244	Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv1020626	chr5:13798819-14177235	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv1015479	chr5:13798819-14180804	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	esv2760949	chr5:13798819-14182550	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv1017356	chr5:13798819-14182550	Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1018474	chr5:13798819-14184599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv1024037	chr5:13798819-14185039	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	nsv1030787	chr5:13799381-14180804	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1018784	chr5:13815834-14178505	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
15	nsv537672	chr5:13815834-14178505	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
16	nsv530219	chr5:13829361-14168901	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
17	nsv1027816	chr5:13847043-14172158	Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
18	nsv537673	chr5:13847043-14172158	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	nsv534466	chr5:13847044-14246208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
20	nsv1020258	chr5:13849471-14178505	Genic enhancers Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
21	nsv537674	chr5:13849471-14178505	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
22	esv2752061	chr5:14109455-14178040	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs32979	EMP1	trans	brain	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14115200-14124200	Weak transcription	HMEC	breast
2	chr5:14117400-14120600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:14117600-14120800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:14118400-14119800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:14118400-14120000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr5:14118600-14119800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:14118600-14119800	Enhancers	Fetal Muscle Trunk	muscle
8	chr5:14118600-14119800	Enhancers	Fetal Muscle Leg	muscle
9	chr5:14118600-14120000	Enhancers	Brain Hippocampus Middle	brain
10	chr5:14118600-14120200	Enhancers	Brain Angular Gyrus	brain
11	chr5:14118600-14120400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:14118600-14120600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:14118600-14120600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:14118800-14119800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:14118800-14119800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:14118800-14119800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:14118800-14120200	Enhancers	Fetal Heart	heart
18	chr5:14118800-14120600	Enhancers	Left Ventricle	heart
19	chr5:14119000-14119800	Enhancers	Fetal Brain Female	brain
20	chr5:14119000-14119800	Enhancers	Pancreas	Pancrea
21	chr5:14119200-14120600	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:14119400-14119800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr5:14119400-14119800	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr5:14119400-14119800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr5:14119400-14120200	Enhancers	HSMMtube	muscle
26	chr5:14119400-14120400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr5:14119400-14120400	Enhancers	Brain Substantia Nigra	brain
28	chr5:14119400-14120600	Enhancers	Brain Germinal Matrix	brain
29	chr5:14119400-14122200	Weak transcription	Placenta	Placenta
30	chr5:14119400-14132200	Weak transcription	Psoas Muscle	Psoas
31	chr5:14119600-14120400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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