Variant report

Variant	rs11713763
Chromosome Location	chr3:53160360-53160361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53159175..53161619-chr3:53212406..53215272,2	MCF-7	breast:
2	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
3	chr3:53159803..53162439-chr3:53162979..53165475,2	K562	blood:
4	chr3:53137358..53139996-chr3:53159100..53161040,2	K562	blood:
5	chr3:53159864..53162439-chr3:53163975..53165914,2	K562	blood:
6	chr3:53160152..53162531-chr3:53170013..53171718,2	K562	blood:

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1080500	1.00[ASW][hapmap];0.91[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs11714876	0.83[LWK][hapmap]
rs13088281	1.00[LWK][hapmap]
rs6799185	0.86[TSI][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	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11713763	ITIH4-AS1	cis	lung	GTEx
rs11713763	GNL3	cis	cerebellum	SCAN
rs11713763	QARS	cis	parietal	SCAN
rs11713763	SEMA3G	cis	parietal	SCAN
rs11713763	TMEM110	cis	parietal	SCAN
rs11713763	SPCS1	cis	parietal	SCAN
rs11713763	GNL3	cis	parietal	SCAN
rs11713763	ITIH4	cis	parietal	SCAN
rs11713763	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53137400-53161600	Strong transcription	Fetal Intestine Small	intestine
2	chr3:53142800-53161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53145000-53161400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:53145800-53161200	Strong transcription	Primary hematopoietic stem cells	blood
5	chr3:53147600-53160800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:53148000-53163600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:53148200-53160600	Strong transcription	Fetal Intestine Large	intestine
8	chr3:53148200-53161000	Strong transcription	Fetal Thymus	thymus
9	chr3:53148400-53160400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr3:53148400-53160800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:53148400-53161000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:53148400-53161000	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:53148400-53161200	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:53148400-53161200	Strong transcription	Dnd41	blood
15	chr3:53148400-53161600	Strong transcription	Primary T cells from cord blood	blood
16	chr3:53148400-53163400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:53148600-53160400	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:53148600-53160800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:53148600-53161200	Strong transcription	Liver	Liver
20	chr3:53148800-53160400	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:53148800-53161200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr3:53149200-53160400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:53149200-53161200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:53149400-53160400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:53149400-53160400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:53149600-53161400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:53149600-53162400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:53150000-53161800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:53150800-53160400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:53150800-53160400	Strong transcription	HepG2	liver
31	chr3:53150800-53160800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:53150800-53161000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr3:53151000-53160400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:53151000-53160600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:53151000-53160800	Strong transcription	HMEC	breast
36	chr3:53151000-53160800	Strong transcription	NHLF	lung
37	chr3:53151000-53161000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:53151000-53161000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:53151000-53161000	Strong transcription	NHEK	skin
40	chr3:53151000-53161000	Strong transcription	Osteobl	bone
41	chr3:53151000-53161400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:53151000-53161400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:53151000-53161800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:53151200-53160400	Strong transcription	Placenta	Placenta
45	chr3:53151200-53160600	Strong transcription	GM12878-XiMat	blood
46	chr3:53151200-53160800	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr3:53151800-53160400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:53152800-53163400	Weak transcription	Fetal Brain Male	brain
49	chr3:53153000-53163600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:53154800-53160400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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