Variant report

Variant	rs1783742
Chromosome Location	chr11:101868415-101868416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10750624	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10791543	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10791544	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10791547	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10895222	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10895229	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10895233	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1274899	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1274901	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274902	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1372414	0.85[TSI][hapmap]
rs1441928	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1470195	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596119	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1661412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783741	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508314	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740931	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3858419	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4363558	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4754829	0.82[CHB][hapmap]
rs7112084	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7114321	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122609	0.89[CEU][hapmap];0.81[YRI][hapmap]
rs7942191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942197	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs930469	1.00[ASW][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs976735	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv898333	chr11:101832670-102079986	Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1783742	MMP1	cis	parietal	SCAN
rs1783742	C11orf70	cis	cerebellum	SCAN
rs1783742	KIAA1377	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101821200-101878400	Weak transcription	Brain Anterior Caudate	brain
2	chr11:101827200-101883400	Weak transcription	Aorta	Aorta
3	chr11:101834600-101876000	Weak transcription	Fetal Lung	lung
4	chr11:101842600-101871000	Weak transcription	Brain Substantia Nigra	brain
5	chr11:101847600-101870800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:101851600-101878200	Weak transcription	HUVEC	blood vessel
7	chr11:101851800-101870600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:101852200-101874800	Weak transcription	Brain Hippocampus Middle	brain
9	chr11:101852800-101876000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:101854200-101874800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:101854400-101878200	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:101854800-101877600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:101855200-101874000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:101858400-101878200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:101859200-101869400	Weak transcription	Esophagus	oesophagus
16	chr11:101859400-101878200	Weak transcription	NHLF	lung
17	chr11:101859600-101878400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:101863600-101878200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:101864000-101869600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr11:101864000-101878200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:101864200-101868800	Enhancers	HepG2	liver
22	chr11:101864200-101869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:101864200-101878200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr11:101864200-101878200	Weak transcription	Fetal Brain Female	brain
25	chr11:101864200-101878400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:101864400-101872600	Weak transcription	Brain Angular Gyrus	brain
27	chr11:101864400-101872800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:101865200-101869200	Strong transcription	Adipose Nuclei	Adipose
29	chr11:101866200-101869400	Strong transcription	Ovary	ovary
30	chr11:101866600-101869400	Weak transcription	Lung	lung
31	chr11:101866600-101878400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr11:101867000-101880800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:101867400-101878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr11:101868000-101869200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:101868200-101868600	ZNF genes & repeats	Left Ventricle	heart
36	chr11:101868200-101868800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:101868200-101869200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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