Variant report

Variant	rs2241580
Chromosome Location	chr5:177668965-177668966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:177664686..177666446-chr5:177667061..177669063,2	MCF-7	breast:
2	chr5:177664512..177669563-chr5:177672713..177676620,5	K562	blood:
3	chr5:177665861..177669287-chr5:177672890..177677511,4	MCF-7	breast:
4	chr5:177667122..177671581-chr5:177672725..177675759,6	K562	blood:
5	chr5:177666998..177669633-chr5:177705585..177707860,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11742670	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11746830	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12521401	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2033202	0.81[EUR][1000 genomes]
rs2241581	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973751	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2973752	0.83[EUR][1000 genomes]
rs2973754	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3812092	0.90[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3812093	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56039553	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57478839	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6422346	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6894388	0.83[EUR][1000 genomes];0.81[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	106 gene(s)	inside rSNPs	diseases
5	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
7	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1018031	chr5:177655010-177746378	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv537969	chr5:177655010-177746378	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv883195	chr5:177655194-177690539	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	nsv883196	chr5:177655194-177690978	Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv883197	chr5:177655194-177707204	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	nsv1025291	chr5:177657927-177756215	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv537970	chr5:177657927-177756215	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	nsv527792	chr5:177659075-177675217	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv883198	chr5:177659075-177690539	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
18	nsv883199	chr5:177661902-177717640	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
19	nsv517167	chr5:177665342-177675217	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv883200	chr5:177665342-177717640	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
21	nsv883201	chr5:177665342-177746863	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
22	esv1849204	chr5:177666243-177676831	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2241580	SQSTM1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177661400-177669600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr5:177661600-177671600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:177661800-177669800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr5:177662200-177674800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:177662600-177669600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:177663400-177669200	Enhancers	Colonic Mucosa	Colon
7	chr5:177663600-177669000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:177664000-177669800	Enhancers	Placenta	Placenta
9	chr5:177664200-177669600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:177664200-177669800	Enhancers	Lung	lung
11	chr5:177665200-177669000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:177666000-177669600	Enhancers	Spleen	Spleen
13	chr5:177666400-177669000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr5:177666400-177669000	Enhancers	GM12878-XiMat	blood
15	chr5:177666400-177669400	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:177666400-177670800	Weak transcription	Pancreas	Pancrea
17	chr5:177666400-177673400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:177666400-177675800	Weak transcription	Esophagus	oesophagus
19	chr5:177666800-177669600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:177667000-177669600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr5:177667200-177669000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr5:177667200-177669200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr5:177667400-177669200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:177667400-177669400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:177667400-177669600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr5:177667400-177670000	Enhancers	Fetal Muscle Leg	muscle
27	chr5:177667600-177669000	Enhancers	Dnd41	blood
28	chr5:177667600-177669200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr5:177667600-177669400	Weak transcription	Liver	Liver
30	chr5:177667600-177669800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr5:177667800-177669400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:177668000-177669200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr5:177668200-177669400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr5:177668400-177669000	Enhancers	Fetal Thymus	thymus
35	chr5:177668400-177669200	Enhancers	Primary B cells from peripheral blood	blood
36	chr5:177668400-177669200	Enhancers	Right Atrium	heart
37	chr5:177668400-177669600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:177668400-177670000	Enhancers	Primary hematopoietic stem cells	blood
39	chr5:177668400-177674600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:177668600-177669200	Enhancers	Primary T cells from cord blood	blood
41	chr5:177668600-177670000	Enhancers	Right Ventricle	heart
42	chr5:177668600-177674600	Weak transcription	Thymus	Thymus
43	chr5:177668800-177669200	Enhancers	Primary B cells from cord blood	blood
44	chr5:177668800-177669400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:177668800-177669800	Enhancers	Left Ventricle	heart

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