Variant report

Variant	rs2119734
Chromosome Location	chr11:101803357-101803358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1004352	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10791545	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10791546	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895220	0.86[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10895224	0.96[YRI][hapmap]
rs10895228	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10895231	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11225049	0.87[CHB][hapmap]
rs11225070	0.95[ASN][1000 genomes]
rs11225080	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11225087	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11225093	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12281520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274898	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1274903	0.85[ASN][1000 genomes]
rs12787877	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12802591	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1298710	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1299588	0.85[ASN][1000 genomes]
rs1372414	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1441929	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1622630	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1661409	0.87[CHB][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1661410	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1661411	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1661412	0.81[TSI][hapmap]
rs1783740	0.88[CEU][hapmap];0.87[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2282612	0.87[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4643040	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6590940	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6590941	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68066934	0.95[ASN][1000 genomes]
rs7105709	0.81[ASW][hapmap];0.88[CEU][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7107662	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7122772	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs975810	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052159	chr11:101439655-101853293	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1051457	chr11:101446705-101837650	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv832250	chr11:101617934-101804020	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	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
5	nsv469989	chr11:101790671-101857758	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv556140	chr11:101790671-101857758	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2119734	MMP1	cis	parietal	SCAN
rs2119734	C11orf70	cis	cerebellum	SCAN
rs2119734	KIAA1377	cis	cerebellum	SCAN
rs2119734	KIAA1377	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101787200-101820200	Weak transcription	Brain Substantia Nigra	brain
2	chr11:101787400-101815600	Weak transcription	Adipose Nuclei	Adipose
3	chr11:101787400-101818800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:101787400-101820400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:101787400-101827800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:101787400-101839200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:101787400-101861200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr11:101787400-101866000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr11:101787600-101809200	Weak transcription	A549	lung
10	chr11:101788200-101837800	Weak transcription	HUVEC	blood vessel
11	chr11:101789000-101815200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:101793800-101816000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:101798400-101829200	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:101798800-101806800	Weak transcription	Primary B cells from cord blood	blood
15	chr11:101800400-101815200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:101800400-101816400	Weak transcription	Ovary	ovary
17	chr11:101800400-101826400	Weak transcription	Aorta	Aorta
18	chr11:101800400-101830200	Weak transcription	Fetal Lung	lung
19	chr11:101800600-101811600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:101800600-101820400	Weak transcription	Brain Anterior Caudate	brain
21	chr11:101801000-101815800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:101802000-101805000	Enhancers	Pancreatic Islets	Pancreatic Islet

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