Variant report

Variant	rs17816711
Chromosome Location	chr15:33350534-33350535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33350149..33352593-chr15:33359553..33361062,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1026752	0.84[EUR][1000 genomes]
rs10519781	0.91[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10519788	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10775202	0.96[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10851823	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072124	0.80[JPT][hapmap]
rs11072125	0.80[JPT][hapmap]
rs11072137	0.80[JPT][hapmap]
rs11072170	0.83[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072175	0.96[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072187	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635106	0.80[JPT][hapmap]
rs11635199	0.86[JPT][hapmap]
rs11636399	0.80[JPT][hapmap]
rs11636433	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11639303	0.91[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11854308	0.89[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs11857770	0.80[JPT][hapmap]
rs11857866	0.93[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12439012	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440002	0.96[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12592516	0.81[EUR][1000 genomes]
rs12594676	0.80[JPT][hapmap]
rs12594962	0.80[JPT][hapmap]
rs16963688	0.80[JPT][hapmap]
rs17235533	0.92[CEU][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17235547	0.92[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2219156	0.82[EUR][1000 genomes]
rs2219159	0.80[AMR][1000 genomes]
rs2291064	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2291065	0.87[EUR][1000 genomes]
rs2291066	0.81[EUR][1000 genomes]
rs2306278	0.96[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28446831	0.81[EUR][1000 genomes]
rs28510826	0.84[EUR][1000 genomes]
rs28603193	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28750521	0.92[ASN][1000 genomes]
rs34606248	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4779604	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4779605	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4779606	0.96[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4780074	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167795	0.82[EUR][1000 genomes]
rs7174332	0.80[JPT][hapmap]
rs8033302	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8039005	1.00[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8039517	0.80[JPT][hapmap]
rs8043116	0.80[JPT][hapmap]
rs922510	0.91[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs922511	0.84[CEU][hapmap];0.86[JPT][hapmap];0.86[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
rs17816711	FMN1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33324000-33356800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:33332200-33355200	Weak transcription	Gastric	stomach
3	chr15:33337000-33352000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:33337000-33358000	Weak transcription	Colonic Mucosa	Colon
5	chr15:33337600-33356800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:33337800-33356800	Weak transcription	HSMMtube	muscle
7	chr15:33338800-33355200	Weak transcription	HSMM	muscle
8	chr15:33344000-33356800	Weak transcription	Esophagus	oesophagus
9	chr15:33344000-33356800	Weak transcription	Lung	lung
10	chr15:33345600-33358200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:33345800-33355200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:33345800-33355200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:33348000-33358200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:33348200-33351200	Weak transcription	Osteobl	bone
15	chr15:33348200-33352600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:33348200-33360000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:33348400-33351200	Weak transcription	Fetal Stomach	stomach
18	chr15:33348400-33351200	Weak transcription	NHLF	lung
19	chr15:33348400-33352200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:33348600-33351000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:33348800-33350800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:33348800-33351400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:33348800-33355200	Weak transcription	Thymus	Thymus
24	chr15:33350000-33351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr15:33350200-33355200	Weak transcription	Stomach Mucosa	stomach
26	chr15:33350400-33350600	Strong transcription	Placenta	Placenta
27	chr15:33350400-33358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:33350400-33358800	Weak transcription	Pancreas	Pancrea

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