Variant report

Variant	rs12421595
Chromosome Location	chr11:74029595-74029596
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74020783..74024598-chr11:74028105..74031169,3	MCF-7	breast:
2	chr11:73966765..73967544-chr11:74029095..74029836,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246211	Chromatin interaction
ENSG00000149380	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11236056	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236057	1.00[ASN][1000 genomes]
rs12416880	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417457	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417835	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418009	1.00[CEU][hapmap]
rs12418387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419385	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420538	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421228	1.00[CEU][hapmap]
rs12421564	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17132911	1.00[CEU][hapmap]
rs1975	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36014178	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530709	1.00[CEU][hapmap]
rs57858196	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58030284	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58206408	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58462364	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58557652	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58587692	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59325091	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59749117	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59848587	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60134332	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60610828	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60721424	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61026077	1.00[ASN][1000 genomes]
rs61109636	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120763	1.00[CEU][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12421595	PGM2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 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	chr11:74028000-74031000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:74028200-74029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:74028400-74030400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:74028400-74030800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:74028400-74031000	Enhancers	Osteobl	bone
7	chr11:74028600-74030200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:74028600-74030800	Enhancers	NHDF-Ad	bronchial
9	chr11:74028600-74031000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:74028600-74031800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:74028800-74030800	Enhancers	HSMMtube	muscle
12	chr11:74028800-74038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:74029000-74030800	Enhancers	NH-A	brain
14	chr11:74029000-74034400	Enhancers	HUVEC	blood vessel
15	chr11:74029200-74029600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:74029200-74029800	Enhancers	Psoas Muscle	Psoas
17	chr11:74029200-74029800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:74029200-74030000	Enhancers	Colon Smooth Muscle	Colon
19	chr11:74029200-74030400	Enhancers	NHLF	lung
20	chr11:74029200-74030800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:74029200-74032000	Enhancers	NHEK	skin
22	chr11:74029400-74029600	Enhancers	Left Ventricle	heart
23	chr11:74029400-74029800	Enhancers	Rectal Smooth Muscle	rectum
24	chr11:74029400-74029800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr11:74029400-74030200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr11:74029400-74030200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:74029400-74030600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:74029400-74031000	Enhancers	Hela-S3	cervix
29	chr11:74029400-74031200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr11:74029400-74031800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:74029400-74031800	Enhancers	HMEC	breast
32	chr11:74029400-74032800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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