Variant report

Variant	rs11718446
Chromosome Location	chr3:101552553-101552554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101546905..101548407-chr3:101551219..101553044,2	MCF-7	breast:
2	chr3:101543921..101548093-chr3:101548561..101552657,6	MCF-7	breast:
3	chr3:101543661..101554550-chr3:101566310..101574179,30	MCF-7	breast:
4	chr3:101551332..101553281-chr3:101567720..101569786,2	K562	blood:
5	chr3:101552465..101554960-chr3:101557471..101558980,2	K562	blood:

Variant related genes	Relation type
ENSG00000144802	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1031710	0.85[JPT][hapmap]
rs11707250	0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap]
rs11711903	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap]
rs11712309	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11712748	0.81[JPT][hapmap]
rs11712888	0.82[AFR][1000 genomes]
rs11714444	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap]
rs11717638	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11914318	0.85[JPT][hapmap]
rs11919389	0.85[JPT][hapmap]
rs12633089	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs13059470	0.85[JPT][hapmap]
rs13065944	0.85[JPT][hapmap]
rs13066768	0.85[JPT][hapmap]
rs13069443	0.81[JPT][hapmap]
rs13081846	0.81[JPT][hapmap]
rs13084113	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13085776	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13094753	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap]
rs1460097	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap]
rs17347156	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs17347644	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17411983	0.81[JPT][hapmap]
rs2288272	0.81[JPT][hapmap];0.80[LWK][hapmap]
rs2290859	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap]
rs3094296	0.81[JPT][hapmap]
rs3094297	0.81[JPT][hapmap]
rs34376498	0.85[JPT][hapmap];0.83[MKK][hapmap]
rs35117343	0.85[JPT][hapmap]
rs35850993	0.85[JPT][hapmap]
rs3806653	0.81[JPT][hapmap]
rs3806654	0.81[JPT][hapmap]
rs4342086	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap]
rs7629753	0.81[JPT][hapmap]
rs7651721	0.81[JPT][hapmap]
rs9830943	0.85[JPT][hapmap]

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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11718446	NXPE3	cis	Esophagus Muscularis	GTEx
rs11718446	NIT2	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101546800-101553000	Weak transcription	Spleen	Spleen
2	chr3:101547000-101561000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:101548200-101552600	Weak transcription	Colonic Mucosa	Colon
4	chr3:101548200-101560800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:101548200-101560800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:101548200-101565600	Weak transcription	Lung	lung
7	chr3:101548400-101552800	Weak transcription	Gastric	stomach
8	chr3:101548400-101553000	Weak transcription	Esophagus	oesophagus
9	chr3:101548400-101555000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:101548400-101556600	Weak transcription	Fetal Stomach	stomach
11	chr3:101548400-101560800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:101548400-101560800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:101548400-101562000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:101548600-101552600	Weak transcription	Fetal Thymus	thymus
15	chr3:101548600-101554200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:101548600-101554200	Weak transcription	Aorta	Aorta
17	chr3:101548600-101555200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:101548600-101555600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:101548600-101555800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:101548600-101555800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:101548600-101555800	Weak transcription	Osteobl	bone
22	chr3:101548600-101556200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:101548600-101559000	Weak transcription	HSMM	muscle
24	chr3:101548600-101560800	Weak transcription	HSMMtube	muscle
25	chr3:101548600-101561000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:101548600-101567000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:101548800-101552600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:101548800-101553800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:101548800-101555800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:101548800-101555800	Weak transcription	Brain Angular Gyrus	brain
31	chr3:101548800-101555800	Weak transcription	Fetal Intestine Small	intestine
32	chr3:101549000-101552600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:101549000-101553000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr3:101549000-101554600	Weak transcription	Brain Substantia Nigra	brain
35	chr3:101549000-101554800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:101549000-101555800	Weak transcription	Brain Anterior Caudate	brain
37	chr3:101549000-101556400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:101549000-101566600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:101549000-101567600	Weak transcription	Primary T cells from cord blood	blood
40	chr3:101549200-101552600	Weak transcription	Primary B cells from cord blood	blood
41	chr3:101549200-101554600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:101549200-101555600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:101549200-101556000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:101549400-101555000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:101550400-101555200	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:101550800-101555200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
47	chr3:101551800-101552600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:101551800-101553200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:101551800-101553800	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr3:101551800-101553800	Enhancers	Sigmoid Colon	Sigmoid Colon

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