Variant report

Variant	rs11573662
Chromosome Location	chr9:110063197-110063198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110060441..110063203-chr9:110064051..110066274,3	MCF-7	breast:
2	chr9:110060491..110063428-chr9:110066349..110068184,2	MCF-7	breast:
3	chr9:110058012..110060076-chr9:110062055..110063823,2	MCF-7	breast:
4	chr9:110062306..110064844-chr9:110068652..110070253,2	K562	blood:
5	chr9:110060398..110063289-chr9:110066758..110069603,2	MCF-7	breast:
6	chr9:110043397..110048376-chr9:110058875..110065071,10	K562	blood:
7	chr9:110044258..110048385-chr9:110059208..110064151,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10868	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573607	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573665	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573703	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573709	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs11573711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11573721	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379885	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12379895	1.00[ASN][1000 genomes]
rs13287251	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805331	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593991	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34731486	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34745099	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35218924	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35494237	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35626978	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35827173	1.00[ASN][1000 genomes]
rs35865856	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35967129	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36016101	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089467	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56161943	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66495692	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66539130	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67630898	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71495992	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716004	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11573662	IKBKAP	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110047600-110067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:110048800-110067800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:110048800-110069600	Weak transcription	Fetal Brain Male	brain
4	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:110049200-110067000	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:110049400-110067800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:110050200-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:110051200-110066000	Weak transcription	Fetal Intestine Large	intestine
10	chr9:110051200-110067000	Weak transcription	Thymus	Thymus
11	chr9:110051600-110079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:110052000-110066800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr9:110052600-110063200	Weak transcription	Placenta	Placenta
14	chr9:110052600-110067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:110052600-110067000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:110052600-110068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:110052600-110068600	Weak transcription	Brain Germinal Matrix	brain
18	chr9:110052600-110068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:110052600-110069200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr9:110052800-110066000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:110053400-110068600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr9:110053600-110063200	Weak transcription	Fetal Thymus	thymus
23	chr9:110053600-110063400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:110055600-110067600	Weak transcription	HSMMtube	muscle
25	chr9:110055600-110068600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:110055800-110068600	Weak transcription	Fetal Brain Female	brain
27	chr9:110055800-110068600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr9:110056400-110063400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:110056800-110065800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr9:110056800-110068600	Weak transcription	Lung	lung
31	chr9:110057200-110066800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr9:110057200-110067000	Weak transcription	Fetal Stomach	stomach
33	chr9:110057200-110067000	Weak transcription	Left Ventricle	heart
34	chr9:110057200-110068800	Weak transcription	Brain Substantia Nigra	brain
35	chr9:110057200-110079200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:110057400-110063600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:110057400-110068600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr9:110057400-110068600	Weak transcription	Esophagus	oesophagus
39	chr9:110057400-110068600	Weak transcription	Gastric	stomach
40	chr9:110057400-110074600	Weak transcription	Spleen	Spleen
41	chr9:110057400-110074800	Weak transcription	Psoas Muscle	Psoas
42	chr9:110057600-110063200	Weak transcription	Primary B cells from cord blood	blood
43	chr9:110058000-110068600	Weak transcription	Aorta	Aorta
44	chr9:110058200-110063400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:110058400-110063200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:110058600-110068600	Weak transcription	Right Ventricle	heart
47	chr9:110058600-110074800	Weak transcription	Right Atrium	heart
48	chr9:110058600-110098600	Weak transcription	Small Intestine	intestine
49	chr9:110059800-110063400	Weak transcription	Ovary	ovary
50	chr9:110059800-110068600	Weak transcription	Pancreas	Pancrea

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