Variant report

Variant	rs9812540
Chromosome Location	chr3:50479107-50479108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50478507..50481167-chr3:50588405..50590760,2	K562	blood:
2	chr3:50373433..50376218-chr3:50478775..50480671,2	MCF-7	breast:
3	chr3:50471606..50474364-chr3:50476758..50479663,3	K562	blood:
4	chr3:50478777..50481371-chr3:50494134..50496538,2	K562	blood:
5	chr3:50478466..50481010-chr3:50538966..50541779,3	MCF-7	breast:
6	chr3:50473646..50476114-chr3:50476289..50479526,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068028	Chromatin interaction
ENSG00000007402	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1034409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2157328	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2187815	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2236966	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2236969	0.94[ASN][1000 genomes]
rs2236970	0.94[ASN][1000 genomes]
rs2236972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2236976	0.97[ASN][1000 genomes]
rs2236977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2236978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2236980	1.00[ASN][1000 genomes]
rs2236982	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2236985	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs2236990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2282757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2282761	1.00[ASN][1000 genomes]
rs28428559	0.94[ASN][1000 genomes]
rs28493735	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28580410	0.94[ASN][1000 genomes]
rs3213520	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58462551	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs59167171	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs59619552	0.94[ASN][1000 genomes]
rs60391761	0.94[ASN][1000 genomes]
rs60697422	0.97[ASN][1000 genomes]
rs61493458	1.00[ASN][1000 genomes]
rs6767505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs73833363	0.94[ASN][1000 genomes]
rs73835503	0.97[ASN][1000 genomes]
rs743754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs743859	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7626470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7642779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7647409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7649603	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9311451	0.97[ASN][1000 genomes]
rs9311453	0.97[ASN][1000 genomes]
rs9311455	0.97[ASN][1000 genomes]
rs9814606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9815761	1.00[YRI][hapmap]
rs9817768	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9826083	1.00[YRI][hapmap]
rs9828829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9829599	0.81[AFR][1000 genomes]
rs9832993	1.00[ASN][1000 genomes]
rs9834579	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9834856	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9837658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9837861	0.94[ASN][1000 genomes]
rs9838849	1.00[YRI][hapmap]
rs9839266	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9839996	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9843693	1.00[ASN][1000 genomes]
rs9854585	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9858351	0.81[AFR][1000 genomes]
rs9863307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9863857	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs9875233	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9880285	1.00[ASN][1000 genomes]
rs9883635	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9990256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
5	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
7	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
8	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
10	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	esv3445182	chr3:50458687-50496660	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50465600-50485800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:50465800-50487000	Weak transcription	Fetal Intestine Small	intestine
3	chr3:50468800-50480200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:50471200-50479800	Enhancers	Fetal Heart	heart
5	chr3:50471600-50479600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:50473200-50483800	Enhancers	Fetal Muscle Leg	muscle
7	chr3:50474000-50479200	Weak transcription	Right Ventricle	heart
8	chr3:50474000-50487400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:50475400-50484200	Weak transcription	Spleen	Spleen
10	chr3:50476200-50480600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:50476600-50481800	Enhancers	Brain Germinal Matrix	brain
12	chr3:50477000-50481600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:50477200-50479200	Weak transcription	Stomach Mucosa	stomach
14	chr3:50477600-50480600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:50477800-50486400	Enhancers	Fetal Muscle Trunk	muscle
16	chr3:50478000-50481800	Enhancers	Placenta	Placenta
17	chr3:50478000-50482800	Enhancers	Lung	lung
18	chr3:50478600-50479400	Enhancers	Right Atrium	heart
19	chr3:50478600-50481400	Enhancers	Fetal Brain Female	brain
20	chr3:50478800-50479800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:50478800-50480200	Enhancers	Fetal Lung	lung
22	chr3:50478800-50481000	Enhancers	HSMMtube	muscle
23	chr3:50479000-50479200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:50479000-50479200	Enhancers	Brain Hippocampus Middle	brain
25	chr3:50479000-50481400	Enhancers	Left Ventricle	heart
26	chr3:50479000-50485000	Enhancers	Gastric	stomach

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