Variant report

Variant	rs3888908
Chromosome Location	chr11:74033066-74033067
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:73966573..73967397-chr11:74032619..74033168,2	MCF-7	breast:
2	chr11:74019898..74022281-chr11:74031863..74033488,2	K562	blood:
3	chr11:73966201..73967800-chr11:74032250..74033563,10	MCF-7	breast:
4	chr11:74010435..74013367-chr11:74031696..74033366,2	MCF-7	breast:
5	chr11:74032300..74033169-chr11:74159606..74160900,3	MCF-7	breast:
6	chr11:73966608..73967238-chr11:74032645..74033232,2	K562	blood:
7	chr11:74032580..74033199-chr8:100370794..100371470,2	MCF-7	breast:
8	chr11:73994107..73996147-chr11:74030507..74033289,2	MCF-7	breast:

No data

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10431176	0.83[CEU][hapmap];0.87[CHD][hapmap]
rs10459047	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898962	0.83[CEU][hapmap];0.87[CHD][hapmap]
rs10898966	0.83[CEU][hapmap];0.84[CHD][hapmap]
rs10898973	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898974	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10898975	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10898976	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10898980	1.00[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs11236029	0.83[CEU][hapmap];0.87[CHD][hapmap]
rs11236042	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11236043	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11236044	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11236052	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11236053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11236054	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236055	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11236060	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11236063	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11236071	1.00[CEU][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs11236077	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs11236092	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs11600314	0.87[CHD][hapmap]
rs11602451	0.87[CHD][hapmap]
rs11604713	0.87[CHD][hapmap]
rs11608147	0.87[CHD][hapmap]
rs12049823	0.85[CEU][hapmap]
rs12225446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17132964	1.00[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1944971	0.83[CEU][hapmap];0.87[CHD][hapmap]
rs2178000	0.87[CHD][hapmap]
rs2282488	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3741132	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3741133	0.83[CEU][hapmap];0.87[CHD][hapmap]
rs3819114	0.85[EUR][1000 genomes]
rs3894652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4121668	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs515924	0.85[CEU][hapmap]
rs550552	0.92[CEU][hapmap]
rs58852370	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs588725	0.85[CEU][hapmap]
rs61902380	0.85[EUR][1000 genomes]
rs625532	0.91[CEU][hapmap]
rs630078	0.92[CEU][hapmap]
rs639228	0.92[CEU][hapmap]
rs658976	0.92[CEU][hapmap]
rs676103	0.85[CEU][hapmap]
rs7110734	0.87[CHD][hapmap]
rs7117465	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7949639	0.83[CEU][hapmap]
rs7951617	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv555425	chr11:74025055-74034473	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv555429	chr11:74025279-74034473	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3888908	PGM2L1	cis	multi-tissue	Pritchard
rs3888908	P4HA3	cis	cerebellum	SCAN
rs3888908	PPME1	cis	cerebellum	SCAN
rs3888908	UCP2	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74023200-74036800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:74028800-74038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:74029000-74034400	Enhancers	HUVEC	blood vessel
4	chr11:74030200-74034400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr11:74030200-74035400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:74030600-74033200	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:74030800-74036600	Weak transcription	HSMM	muscle
8	chr11:74030800-74037200	Weak transcription	Aorta	Aorta
9	chr11:74031200-74033800	Weak transcription	Lung	lung
10	chr11:74031200-74036200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:74031200-74071200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:74031400-74034400	Enhancers	Osteobl	bone
13	chr11:74031400-74034600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:74031600-74034600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:74031800-74034000	Enhancers	Fetal Brain Male	brain
16	chr11:74032000-74034600	Enhancers	Psoas Muscle	Psoas
17	chr11:74032200-74034000	Enhancers	NHLF	lung
18	chr11:74032400-74034000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:74032600-74033200	Enhancers	Left Ventricle	heart
20	chr11:74032600-74033400	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr11:74032600-74034000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:74032600-74034000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:74032600-74034200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:74032600-74034200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:74032600-74034200	Enhancers	Fetal Lung	lung
26	chr11:74032600-74034400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr11:74032800-74033200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr11:74032800-74033200	Enhancers	Primary B cells from peripheral blood	blood
29	chr11:74032800-74033400	Enhancers	Brain Hippocampus Middle	brain
30	chr11:74032800-74033600	Enhancers	Primary hematopoietic stem cells	blood
31	chr11:74032800-74034000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:74032800-74034000	Enhancers	Fetal Muscle Leg	muscle
33	chr11:74032800-74034200	Enhancers	Stomach Smooth Muscle	stomach
34	chr11:74032800-74034200	Enhancers	NH-A	brain
35	chr11:74032800-74034400	Enhancers	HSMMtube	muscle
36	chr11:74032800-74034600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:74032800-74034800	Enhancers	Adipose Nuclei	Adipose
38	chr11:74032800-74034800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr11:74033000-74033400	Flanking Active TSS	NHDF-Ad	bronchial
40	chr11:74033000-74034000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr11:74033000-74034000	Enhancers	Rectal Smooth Muscle	rectum
42	chr11:74033000-74036600	Weak transcription	Pancreas	Pancrea
43	chr11:74033000-74037000	Weak transcription	Right Ventricle	heart
44	chr11:74033000-74037000	Weak transcription	A549	lung

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