Variant report

Variant	rs62002761
Chromosome Location	chr15:33322781-33322782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:33312970..33316208-chr15:33320262..33322865,3	MCF-7	breast:
2	chr15:33320032..33323364-chr15:33359725..33362232,3	MCF-7	breast:
3	chr15:33321737..33324344-chr15:33359757..33362339,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11072124	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072125	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072131	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072137	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635106	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635199	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636078	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11636399	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854308	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11857770	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857793	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11857821	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11857866	0.92[EUR][1000 genomes]
rs12101826	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592204	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12592516	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12594676	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12594962	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595089	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963688	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963945	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1840400	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2169938	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2219156	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2339178	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28446831	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28464512	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28489655	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28592093	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28592957	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28676777	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28748087	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28750521	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28866011	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61999970	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7167795	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174332	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174340	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028114	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8037860	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039517	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62002761	FMN1	cis	Thyroid	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33315200-33323400	Weak transcription	Esophagus	oesophagus
2	chr15:33315200-33323400	Weak transcription	NH-A	brain
3	chr15:33315200-33329400	Weak transcription	Pancreas	Pancrea
4	chr15:33315400-33335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:33315600-33323600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:33315800-33323200	Weak transcription	HMEC	breast
7	chr15:33317200-33323400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr15:33317200-33324600	Enhancers	NHDF-Ad	bronchial
9	chr15:33317400-33323400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:33318200-33322800	Enhancers	Fetal Thymus	thymus
11	chr15:33318200-33323400	Enhancers	HSMMtube	muscle
12	chr15:33319200-33323200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:33319400-33322800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:33320200-33323400	Weak transcription	NHEK	skin
15	chr15:33320400-33323400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:33320600-33323400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:33320800-33323600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:33320800-33324000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr15:33321000-33322800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr15:33321000-33323200	Weak transcription	Osteobl	bone
21	chr15:33321000-33323600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr15:33321200-33324000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:33321800-33323400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:33321800-33323400	Weak transcription	Psoas Muscle	Psoas
25	chr15:33321800-33323800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:33322000-33323200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:33322000-33323200	Weak transcription	HSMM	muscle
28	chr15:33322000-33323400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:33322000-33323400	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:33322000-33323400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:33322000-33324000	Enhancers	Thymus	Thymus
32	chr15:33322000-33326000	Weak transcription	Colonic Mucosa	Colon
33	chr15:33322400-33330000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:33322600-33322800	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr15:33322600-33323400	Weak transcription	NHLF	lung
36	chr15:33322600-33326200	Weak transcription	Stomach Mucosa	stomach

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