Variant report

Variant	rs12420538
Chromosome Location	chr11:74091457-74091458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74087058..74089421-chr11:74090926..74093848,2	MCF-7	breast:
2	chr11:74091071..74093515-chr11:74095775..74098618,2	K562	blood:
3	chr11:74090302..74094852-chr11:74107852..74111115,4	MCF-7	breast:
4	chr11:74085550..74088254-chr11:74088597..74091470,2	K562	blood:

Variant related genes	Relation type
ENSG00000165434	Chromatin interaction
ENSG00000264402	Chromatin interaction
ENSG00000254631	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11236056	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236057	1.00[ASN][1000 genomes]
rs12416880	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417457	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417458	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417835	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418387	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421595	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36014178	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57858196	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58030284	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58206408	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58462364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58557652	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58587692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59325091	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59749117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59848587	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60134332	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60610828	1.00[ASN][1000 genomes]
rs60721424	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61026077	1.00[ASN][1000 genomes]
rs61109636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv1049915	chr11:74052264-74126319	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
7	nsv524552	chr11:74080107-74092403	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12420538	PGM2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74068800-74094800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:74072000-74092200	Weak transcription	Lung	lung
3	chr11:74072000-74095800	Weak transcription	Aorta	Aorta
4	chr11:74072200-74097000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:74072400-74093200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:74072400-74108000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:74072800-74098200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:74075400-74095000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:74078600-74096200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:74079000-74092400	Weak transcription	Psoas Muscle	Psoas
11	chr11:74079200-74092200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:74079200-74094000	Weak transcription	Left Ventricle	heart
13	chr11:74079400-74092200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:74079400-74105000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:74079800-74093800	Weak transcription	Fetal Lung	lung
16	chr11:74080200-74092000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:74080600-74098000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:74081000-74104000	Weak transcription	Fetal Brain Female	brain
19	chr11:74081400-74105000	Weak transcription	Thymus	Thymus
20	chr11:74081600-74095200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:74081800-74095000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:74081800-74108200	Weak transcription	Primary B cells from cord blood	blood
23	chr11:74083200-74091800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:74083200-74091800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:74083200-74092200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:74084000-74108200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:74084400-74099800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr11:74084600-74099600	Weak transcription	Primary T cells from cord blood	blood
29	chr11:74084600-74108200	Weak transcription	HSMMtube	muscle
30	chr11:74084800-74091800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:74085000-74092000	Weak transcription	A549	lung
32	chr11:74085000-74092200	Weak transcription	NH-A	brain
33	chr11:74085000-74100000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr11:74085200-74092200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:74085400-74107800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr11:74085600-74099600	Weak transcription	HUVEC	blood vessel
37	chr11:74085800-74100000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:74086200-74099800	Weak transcription	Fetal Thymus	thymus
39	chr11:74087400-74108200	Weak transcription	HSMM	muscle
40	chr11:74091000-74092200	Weak transcription	Pancreas	Pancrea

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