Variant report

Variant	rs58206408
Chromosome Location	chr11:74099697-74099698
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:74099483..74099994-chr11:74153863..74154588,2	MCF-7	breast:
2	chr11:74099605..74100422-chr11:74153909..74154835,7	MCF-7	breast:
3	chr11:74082494..74084345-chr11:74098312..74100057,2	MCF-7	breast:
4	chr11:74097990..74101024-chr11:74102586..74104260,4	K562	blood:
5	chr11:74099650..74100358-chr11:74160062..74160991,4	MCF-7	breast:
6	chr11:74099388..74100488-chr11:74160054..74161057,5	MCF-7	breast:
7	chr11:74099429..74100351-chr11:74159564..74161010,6	K562	blood:
8	chr11:74097699..74100088-chr11:74103636..74105838,4	MCF-7	breast:
9	chr11:74043932..74046437-chr11:74097322..74099844,2	K562	blood:
10	chr11:73966846..73967553-chr11:74099341..74100160,2	MCF-7	breast:

No data

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11236056	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236057	1.00[ASN][1000 genomes]
rs12416880	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417457	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417458	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12417835	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418387	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12419385	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420538	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421564	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421595	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36014178	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57858196	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58030284	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58462364	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58557652	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58587692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59325091	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59749117	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59848587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60134332	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60610828	1.00[ASN][1000 genomes]
rs60721424	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61026077	1.00[ASN][1000 genomes]
rs61109636	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58206408	PGM2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74072400-74108000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr11:74079400-74105000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr11:74081000-74104000	Weak transcription	Fetal Brain Female	brain
4	chr11:74081400-74105000	Weak transcription	Thymus	Thymus
5	chr11:74081800-74108200	Weak transcription	Primary B cells from cord blood	blood
6	chr11:74084000-74108200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:74084400-74099800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:74084600-74108200	Weak transcription	HSMMtube	muscle
9	chr11:74085000-74100000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr11:74085400-74107800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr11:74085800-74100000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:74086200-74099800	Weak transcription	Fetal Thymus	thymus
13	chr11:74087400-74108200	Weak transcription	HSMM	muscle
14	chr11:74092600-74099800	Weak transcription	A549	lung
15	chr11:74092600-74100000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:74092600-74108200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:74093600-74099800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr11:74096000-74104600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:74096000-74108200	Weak transcription	Fetal Intestine Small	intestine
20	chr11:74096400-74100000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr11:74098000-74100200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr11:74098200-74100200	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr11:74098400-74100200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr11:74098600-74100000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:74099200-74100000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:74099600-74099800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr11:74099600-74100200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr11:74099600-74100200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr11:74099600-74100400	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr11:74099600-74100400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:74099600-74100400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:74099600-74100400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr11:74099600-74100400	Enhancers	HUVEC	blood vessel
34	chr11:74099600-74102400	Enhancers	Primary T cells from cord blood	blood
35	chr11:74099600-74103200	Enhancers	Primary T helper cells PMA-I stimulated	--

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