Variant report

Variant	rs4647516
Chromosome Location	chr9:97887988-97887989
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97809551..97811519-chr9:97887911..97889998,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

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[ASN][1000 genomes]
rs35108112	1.00[ASN][1000 genomes]
rs3780566	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]
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]
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]
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]
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]
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]
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[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]
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]
rs60228132	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61358915	1.00[AFR][1000 genomes]
rs7037729	1.00[ASN][1000 genomes]
rs73528484	1.00[AFR][1000 genomes]
rs73528487	1.00[AFR][1000 genomes]
rs73530498	1.00[ASN][1000 genomes]
rs73532103	1.00[ASN][1000 genomes]
rs73534874	0.93[AFR][1000 genomes]
rs73534875	0.93[AFR][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]
rs7854840	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7859625	1.00[YRI][hapmap];1.00[AFR][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:92 , 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	chr9:97861200-97889800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:97866000-97889600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:97866200-97889600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:97868600-97889400	Weak transcription	Fetal Heart	heart
6	chr9:97869800-97889800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr9:97870400-97889600	Weak transcription	Fetal Thymus	thymus
8	chr9:97870600-97889800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:97874600-97889400	Weak transcription	Colonic Mucosa	Colon
10	chr9:97875000-97889800	Weak transcription	Hela-S3	cervix
11	chr9:97875200-97889600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:97875200-97889600	Weak transcription	HSMMtube	muscle
13	chr9:97875400-97889400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:97875400-97889400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:97875400-97895400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:97875400-97900400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:97875600-97889400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:97875600-97889600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:97875600-97889600	Weak transcription	Adipose Nuclei	Adipose
20	chr9:97875600-97900000	Weak transcription	Spleen	Spleen
21	chr9:97875600-97906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr9:97875800-97888800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:97875800-97892200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:97876800-97889600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:97877000-97889600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:97877000-97889600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:97877000-97892000	Weak transcription	Gastric	stomach
28	chr9:97877000-97896400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:97879000-97889200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr9:97879200-97888800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr9:97879200-97889400	Weak transcription	HSMM	muscle
32	chr9:97879200-97889600	Weak transcription	Right Atrium	heart
33	chr9:97879400-97889400	Weak transcription	Left Ventricle	heart
34	chr9:97879400-97889400	Weak transcription	Pancreas	Pancrea
35	chr9:97879600-97889200	Weak transcription	Brain Substantia Nigra	brain
36	chr9:97879600-97889400	Weak transcription	Brain Angular Gyrus	brain
37	chr9:97879600-97889600	Weak transcription	Ovary	ovary
38	chr9:97879600-97890600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:97879800-97888000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:97879800-97889200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:97879800-97889600	Weak transcription	GM12878-XiMat	blood
42	chr9:97880200-97889600	Strong transcription	Liver	Liver
43	chr9:97881400-97888000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr9:97881400-97889000	Weak transcription	Aorta	Aorta
45	chr9:97881400-97889600	Weak transcription	Fetal Brain Male	brain
46	chr9:97881400-97889600	Weak transcription	Fetal Brain Female	brain
47	chr9:97883800-97889400	Weak transcription	Colon Smooth Muscle	Colon
48	chr9:97884000-97888000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr9:97884000-97889200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr9:97884000-97889400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links