Variant report

Variant	rs12550873
Chromosome Location	chr9:93573597-93573598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93561656..93565893-chr9:93566155..93575937,12	MCF-7	breast:
2	chr9:93571707..93573621-chr9:93620166..93622474,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11792561	0.81[CEU][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005463	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552742	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12682953	1.00[ASN][1000 genomes]
rs12685847	1.00[ASN][1000 genomes]
rs12686576	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331504	1.00[ASN][1000 genomes]
rs1460836	1.00[ASN][1000 genomes]
rs17454793	1.00[ASN][1000 genomes]
rs2065583	0.88[CEU][hapmap]
rs290237	0.83[ASW][hapmap]
rs290238	0.83[ASW][hapmap]
rs60044325	0.81[AMR][1000 genomes]
rs61388775	0.81[AMR][1000 genomes]
rs62558478	1.00[ASN][1000 genomes]
rs62558479	1.00[ASN][1000 genomes]
rs62558496	1.00[ASN][1000 genomes]
rs62558501	1.00[ASN][1000 genomes]
rs62558503	1.00[ASN][1000 genomes]
rs62558550	1.00[ASN][1000 genomes]
rs62558551	1.00[ASN][1000 genomes]
rs62558552	1.00[ASN][1000 genomes]
rs62558553	1.00[ASN][1000 genomes]
rs62558555	1.00[ASN][1000 genomes]
rs62558557	1.00[ASN][1000 genomes]
rs62559062	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559063	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019286	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046491	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv893569	chr9:93552550-93587089	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	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
rs12550873	ISCA1	cis	parietal	SCAN

Chromatin state (count:38 , 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	chr9:93565400-93577000	Weak transcription	Colonic Mucosa	Colon
3	chr9:93567800-93584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:93567800-93584800	Weak transcription	Fetal Intestine Large	intestine
5	chr9:93567800-93597400	Weak transcription	Gastric	stomach
6	chr9:93568400-93575000	Enhancers	Fetal Thymus	thymus
7	chr9:93568400-93576600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:93568600-93573600	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr9:93569600-93574600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:93571000-93575200	Strong transcription	Fetal Intestine Small	intestine
11	chr9:93571200-93574000	Weak transcription	Pancreas	Pancrea
12	chr9:93571200-93576200	Genic enhancers	Primary monocytes fromperipheralblood	blood
13	chr9:93571200-93576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:93571400-93576600	Weak transcription	Small Intestine	intestine
15	chr9:93571400-93576800	Weak transcription	Primary T cells from cord blood	blood
16	chr9:93571600-93575800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr9:93571800-93577600	Weak transcription	Fetal Kidney	kidney
18	chr9:93572000-93576000	Genic enhancers	Monocytes-CD14+_RO01746	blood
19	chr9:93572400-93575000	Enhancers	Stomach Mucosa	stomach
20	chr9:93572600-93574200	Enhancers	HMEC	breast
21	chr9:93572600-93575400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:93572600-93591000	Weak transcription	Lung	lung
23	chr9:93572800-93574400	Weak transcription	Thymus	Thymus
24	chr9:93572800-93574600	Weak transcription	Spleen	Spleen
25	chr9:93572800-93576800	Weak transcription	Esophagus	oesophagus
26	chr9:93572800-93584800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:93573000-93574000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr9:93573000-93574200	Enhancers	NHEK	skin
29	chr9:93573000-93575400	Weak transcription	Fetal Stomach	stomach
30	chr9:93573200-93573800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:93573200-93574000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:93573200-93574000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr9:93573200-93574400	Weak transcription	Primary B cells from cord blood	blood
34	chr9:93573200-93574400	Enhancers	GM12878-XiMat	blood
35	chr9:93573200-93575800	Weak transcription	K562	blood
36	chr9:93573200-93576600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:93573200-93589600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:93573400-93577200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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