Variant report

Variant	rs3780566
Chromosome Location	chr9:97894864-97894865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97678927..97686235-chr9:97889117..97896057,11	MCF-7	breast:
2	chr9:97681630..97683454-chr9:97893075..97894960,2	MCF-7	breast:
3	chr9:97544700..97548107-chr9:97891004..97896251,5	MCF-7	breast:
4	chr9:97393391..97395196-chr9:97892426..97894999,2	MCF-7	breast:
5	chr9:97459238..97460937-chr9:97893388..97895358,2	MCF-7	breast:
6	chr9:97892364..97896798-chr9:97897558..97901820,5	K562	blood:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1004813	0.88[GIH][hapmap]
rs10512252	0.88[GIH][hapmap]
rs12683030	0.85[JPT][hapmap]
rs12683182	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12684215	1.00[ASN][1000 genomes]
rs12685903	1.00[ASN][1000 genomes]
rs12686588	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1875835	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1886993	1.00[ASN][1000 genomes]
rs2078379	0.88[GIH][hapmap]
rs2121200	1.00[ASN][1000 genomes]
rs2404458	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35108112	1.00[ASN][1000 genomes]
rs3802449	0.85[JPT][hapmap]
rs400727	0.85[JPT][hapmap]
rs4647348	0.89[ASN][1000 genomes]
rs4647352	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647354	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4647360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647367	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647378	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647386	1.00[ASN][1000 genomes]
rs4647387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4647397	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647398	1.00[ASN][1000 genomes]
rs4647402	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647405	1.00[ASN][1000 genomes]
rs4647408	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647414	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647430	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647436	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647437	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647449	1.00[ASN][1000 genomes]
rs4647464	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647465	1.00[ASN][1000 genomes]
rs4647466	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647472	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647473	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647474	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647477	1.00[ASN][1000 genomes]
rs4647484	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647485	1.00[ASN][1000 genomes]
rs4647486	1.00[ASN][1000 genomes]
rs4647487	0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647491	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647493	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647502	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647508	1.00[ASN][1000 genomes]
rs4647509	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4647510	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4647514	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647516	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4647521	0.88[ASN][1000 genomes]
rs4647549	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs57641389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60228132	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61358915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7037729	1.00[ASN][1000 genomes]
rs73528484	1.00[AFR][1000 genomes]
rs73528487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73530498	1.00[ASN][1000 genomes]
rs73532103	1.00[ASN][1000 genomes]
rs73534874	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534875	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534887	1.00[ASN][1000 genomes]
rs73534888	1.00[ASN][1000 genomes]
rs73534896	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs73534898	1.00[ASN][1000 genomes]
rs73539228	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73539285	1.00[AMR][1000 genomes]
rs7854840	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7859625	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9792415	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9792481	1.00[ASN][1000 genomes]
rs9792533	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9792691	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	274 gene(s)	inside rSNPs	diseases
3	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr9:97875400-97895400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:97875400-97900400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr9:97875600-97900000	Weak transcription	Spleen	Spleen
5	chr9:97875600-97906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:97877000-97896400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:97887400-97916400	Weak transcription	Thymus	Thymus
8	chr9:97888000-97900000	Weak transcription	Primary T cells from cord blood	blood
9	chr9:97890000-97895200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:97890000-97898600	Weak transcription	Left Ventricle	heart
11	chr9:97890000-97898600	Weak transcription	Right Atrium	heart
12	chr9:97890000-97900000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:97890000-97906600	Weak transcription	Right Ventricle	heart
14	chr9:97890000-97919600	Weak transcription	Hela-S3	cervix
15	chr9:97890000-97928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:97890200-97895200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr9:97890200-97898400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr9:97890200-97900400	Weak transcription	Esophagus	oesophagus
19	chr9:97890400-97895800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:97890400-97896200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:97890400-97897000	Weak transcription	Colonic Mucosa	Colon
22	chr9:97890400-97902800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr9:97890600-97900000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:97890600-97900000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:97891400-97896000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:97891600-97896000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:97891800-97898200	Enhancers	Liver	Liver
28	chr9:97892200-97896800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:97892400-97896200	Weak transcription	Small Intestine	intestine
30	chr9:97892600-97896400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:97892600-97900400	Weak transcription	Brain Germinal Matrix	brain
32	chr9:97892800-97896400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:97893200-97901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr9:97893400-97895600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr9:97893400-97896600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:97893400-97898200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:97893600-97895000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr9:97893600-97895400	Enhancers	H9 Cell Line	embryonic stem cell
39	chr9:97893600-97895800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr9:97893600-97896200	Enhancers	Fetal Kidney	kidney
41	chr9:97893800-97895400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:97893800-97895400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:97893800-97895400	Weak transcription	Fetal Intestine Small	intestine
44	chr9:97893800-97895800	Weak transcription	Fetal Intestine Large	intestine
45	chr9:97893800-97896400	Weak transcription	Adipose Nuclei	Adipose
46	chr9:97893800-97896600	Weak transcription	HepG2	liver
47	chr9:97893800-97896800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr9:97893800-97896800	Weak transcription	Fetal Brain Male	brain
49	chr9:97893800-97896800	Weak transcription	Fetal Brain Female	brain
50	chr9:97893800-97897000	Weak transcription	Placenta	Placenta

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