Variant report

Variant	rs1840400
Chromosome Location	chr15:33314158-33314159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:33313534..33314713-chr15:33367097..33367829,3	MCF-7	breast:
2	chr15:33310761..33317010-chr15:33354777..33361874,13	MCF-7	breast:
3	chr15:33313321..33315541-chr15:33363936..33365487,2	MCF-7	breast:
4	chr15:33314155..33314778-chr15:33424470..33425220,3	K562	blood:
5	chr15:33313722..33314926-chr15:33367294..33368162,3	MCF-7	breast:
6	chr15:33313879..33314536-chr15:33378426..33379023,2	MCF-7	breast:
7	chr15:33312970..33316208-chr15:33320262..33322865,3	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	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072131	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072137	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11635106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11635199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636078	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11636399	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854308	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11857770	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11857793	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11857821	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11857866	0.90[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12101826	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592204	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12592516	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12594676	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595089	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16963688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16963945	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2169938	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2219156	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2339178	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28446831	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28464512	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28489655	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28592093	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28592957	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28676777	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28748087	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28750521	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28866011	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61999970	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62002761	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7167795	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7174332	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7174340	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028114	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8037860	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039517	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8041317	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8043116	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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
rs1840400	FMN1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33300400-33314200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:33300600-33314400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr15:33301600-33314400	Weak transcription	Gastric	stomach
4	chr15:33302200-33314400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:33306600-33314400	Weak transcription	NH-A	brain
6	chr15:33306600-33314800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:33306800-33314200	Weak transcription	HSMM	muscle
8	chr15:33306800-33314400	Weak transcription	Osteobl	bone
9	chr15:33306800-33321000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:33307000-33314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:33307200-33314200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:33307200-33314800	Weak transcription	Colonic Mucosa	Colon
13	chr15:33308000-33314200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:33309000-33314400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:33309400-33314400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:33309600-33314400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:33309600-33316200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:33309800-33314200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:33309800-33314200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:33310600-33314600	Weak transcription	Brain Angular Gyrus	brain
21	chr15:33311000-33314200	Weak transcription	HSMMtube	muscle
22	chr15:33311000-33314400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:33311000-33314400	Weak transcription	NHLF	lung
24	chr15:33311200-33314400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:33311200-33314400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:33311200-33318000	Weak transcription	Thymus	Thymus
27	chr15:33312400-33314400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:33312400-33314800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:33312600-33317200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:33312800-33314400	Weak transcription	Fetal Thymus	thymus
31	chr15:33313000-33314600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:33313400-33315400	Enhancers	Stomach Mucosa	stomach
33	chr15:33313600-33315200	Enhancers	Brain Substantia Nigra	brain
34	chr15:33313800-33315400	Enhancers	Brain Hippocampus Middle	brain
35	chr15:33314000-33314200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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