Variant report

Variant	rs2013826
Chromosome Location	chr9:93591279-93591280
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93563668..93565517-chr9:93590298..93592693,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1081767	0.86[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs1172681	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs167078	0.86[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs169724	0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs182361	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs187306	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs188312	0.86[ASN][1000 genomes]
rs2065583	0.81[MKK][hapmap]
rs290211	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs290212	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs290214	0.95[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs290215	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs290216	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs290217	0.90[ASN][1000 genomes]
rs290218	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs290219	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs290245	0.85[ASN][1000 genomes]
rs290246	0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs290247	0.86[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs290248	0.85[ASN][1000 genomes]
rs290249	0.85[ASN][1000 genomes]
rs290250	0.83[ASN][1000 genomes]
rs290251	0.82[ASN][1000 genomes]
rs290252	0.83[ASN][1000 genomes]
rs290974	0.91[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs290975	0.86[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs290976	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs290984	0.81[ASN][1000 genomes]
rs4744505	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs745743	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs772410	0.86[ASN][1000 genomes]
rs913980	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893567	chr9:93519280-93609668	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2013826	ISCA1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:93567800-93597400	Weak transcription	Gastric	stomach
3	chr9:93577000-93598800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:93577800-93606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:93578600-93592400	Weak transcription	Esophagus	oesophagus
6	chr9:93580800-93603400	Weak transcription	K562	blood
7	chr9:93581200-93593400	Weak transcription	Stomach Mucosa	stomach
8	chr9:93582600-93595200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:93583000-93599600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:93585400-93593200	Weak transcription	Fetal Intestine Small	intestine
11	chr9:93585400-93594600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:93585400-93594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:93585600-93607800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:93589200-93592200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr9:93589200-93592400	Weak transcription	Spleen	Spleen
16	chr9:93589200-93606000	Weak transcription	Colonic Mucosa	Colon
17	chr9:93589600-93592600	Weak transcription	Thymus	Thymus
18	chr9:93589800-93592400	Weak transcription	Fetal Stomach	stomach
19	chr9:93590000-93593200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:93590000-93601600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:93590200-93591600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:93590200-93591800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:93590400-93591400	Enhancers	Primary hematopoietic stem cells	blood
24	chr9:93590400-93593600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr9:93590600-93591400	Enhancers	Small Intestine	intestine
26	chr9:93590600-93591800	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr9:93590800-93591400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:93590800-93591400	Flanking Active TSS	GM12878-XiMat	blood
29	chr9:93590800-93591800	Genic enhancers	Monocytes-CD14+_RO01746	blood
30	chr9:93591000-93599600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:93591000-93603200	Weak transcription	Fetal Kidney	kidney
32	chr9:93591200-93592200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr9:93591200-93592400	Weak transcription	Fetal Thymus	thymus
34	chr9:93591200-93592400	Weak transcription	Lung	lung
35	chr9:93591200-93592400	Weak transcription	Pancreas	Pancrea
36	chr9:93591200-93592600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr9:93591200-93593600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr9:93591200-93595000	Weak transcription	Adipose Nuclei	Adipose
39	chr9:93591200-93596400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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