Variant report

Variant	rs4245453
Chromosome Location	chr11:77533652-77533653
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:77532998..77535341-chr11:77537049..77538948,2	K562	blood:
2	chr11:77345294..77350451-chr11:77530428..77533693,5	K562	blood:
3	chr11:77530218..77533723-chr11:77703658..77708132,10	MCF-7	breast:
4	chr11:77528468..77531025-chr11:77533622..77535888,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149262	Chromatin interaction
ENSG00000074201	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10698394	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10793262	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10793263	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10793264	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899398	0.81[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899402	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899403	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899405	0.83[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10899406	0.87[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10899407	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10899408	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899409	0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11237284	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11237289	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11237295	0.81[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237299	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237303	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11518811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12222530	0.82[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12364072	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12794428	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1613945	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1783546	0.83[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790235	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1790240	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790246	0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790250	0.84[JPT][hapmap]
rs1793334	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793336	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1793341	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1793343	0.82[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs2013296	0.81[MEX][hapmap];0.85[MKK][hapmap]
rs2034499	0.82[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs2212317	0.83[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2298819	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2510967	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4638330	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945198	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945201	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945206	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs496786	0.84[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs574665	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61900164	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592741	0.85[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap]
rs672460	0.88[ASW][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs7110670	0.91[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs7110924	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7128224	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7130719	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7358471	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7925343	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7927913	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7931272	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7938133	0.93[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs7940734	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7946637	0.81[MEX][hapmap];0.85[MKK][hapmap]
rs9666484	0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9988883	0.83[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4245453	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs4245453	INTS4	cis	cerebellum	SCAN
rs4245453	AQP11	cis	parietal	SCAN
rs4245453	PAK1	cis	cerebellum	SCAN
rs4245453	INTS4	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77530000-77534400	Active TSS	A549	lung
2	chr11:77530400-77533800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:77532600-77534600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:77532800-77534200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:77533000-77534400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr11:77533000-77534400	Weak transcription	Placenta	Placenta
7	chr11:77533000-77534400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:77533000-77534600	Weak transcription	Aorta	Aorta
9	chr11:77533000-77534800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:77533000-77534800	Weak transcription	Brain Anterior Caudate	brain
11	chr11:77533000-77535000	Enhancers	Fetal Heart	heart
12	chr11:77533000-77537600	Weak transcription	Thymus	Thymus
13	chr11:77533000-77544400	Weak transcription	Primary B cells from cord blood	blood
14	chr11:77533000-77553800	Weak transcription	Brain Angular Gyrus	brain
15	chr11:77533000-77554000	Weak transcription	Brain Substantia Nigra	brain
16	chr11:77533000-77554200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:77533200-77534200	Enhancers	Fetal Stomach	stomach
18	chr11:77533200-77534400	Weak transcription	HSMMtube	muscle
19	chr11:77533200-77535400	Enhancers	Liver	Liver
20	chr11:77533400-77533800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:77533400-77533800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:77533400-77533800	Enhancers	Adipose Nuclei	Adipose
23	chr11:77533400-77533800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr11:77533400-77534000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:77533400-77534200	Weak transcription	Lung	lung
26	chr11:77533400-77534400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:77533400-77534400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:77533400-77534400	Weak transcription	Colon Smooth Muscle	Colon
29	chr11:77533400-77534400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:77533400-77534400	Weak transcription	Fetal Intestine Large	intestine
31	chr11:77533400-77534400	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:77533400-77534400	Weak transcription	Psoas Muscle	Psoas
33	chr11:77533400-77534400	Weak transcription	Right Atrium	heart
34	chr11:77533400-77534400	Weak transcription	Stomach Mucosa	stomach
35	chr11:77533400-77534400	Weak transcription	K562	blood
36	chr11:77533400-77534600	Weak transcription	Fetal Kidney	kidney
37	chr11:77533400-77534800	Weak transcription	HSMM	muscle
38	chr11:77533400-77535000	Enhancers	Fetal Lung	lung
39	chr11:77533400-77535000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:77533400-77535000	Weak transcription	Hela-S3	cervix
41	chr11:77533400-77535000	Weak transcription	NHDF-Ad	bronchial
42	chr11:77533400-77535400	Enhancers	Osteobl	bone
43	chr11:77533400-77535600	Weak transcription	Right Ventricle	heart
44	chr11:77533400-77552200	Weak transcription	Brain Hippocampus Middle	brain
45	chr11:77533400-77552200	Weak transcription	Left Ventricle	heart
46	chr11:77533400-77553800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:77533400-77554000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr11:77533400-77565600	Weak transcription	Gastric	stomach
49	chr11:77533400-77565600	Weak transcription	Pancreas	Pancrea
50	chr11:77533600-77533800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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