Variant report

Variant	rs4647408
Chromosome Location	chr9:98012749-98012750
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	chr9:98010532..98014660-chr9:98272495..98275814,3	K562	blood:
2	chr9:98007562..98009225-chr9:98010300..98012768,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12683030	0.85[JPT][hapmap]
rs12683182	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][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[MKK][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]
rs2121200	1.00[ASN][1000 genomes]
rs2404458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35108112	1.00[ASN][1000 genomes]
rs3780566	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];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];1.00[MKK][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]
rs4647414	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[ASN][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]
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]
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[MKK][hapmap];1.00[ASN][1000 genomes]
rs4647485	1.00[ASN][1000 genomes]
rs4647486	1.00[ASN][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[MKK][hapmap];1.00[ASN][1000 genomes]
rs4647508	1.00[ASN][1000 genomes]
rs4647509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647510	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647514	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs4647516	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];1.00[MKK][hapmap]
rs60228132	1.00[ASN][1000 genomes]
rs7037729	1.00[ASN][1000 genomes]
rs73530498	1.00[ASN][1000 genomes]
rs73532103	1.00[ASN][1000 genomes]
rs73534887	1.00[ASN][1000 genomes]
rs73534888	1.00[ASN][1000 genomes]
rs73534896	0.89[ASN][1000 genomes]
rs73534898	1.00[ASN][1000 genomes]
rs7854840	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9792415	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][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[MKK][hapmap];1.00[ASN][1000 genomes]
rs9792691	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97973600-98024000	Weak transcription	Gastric	stomach
2	chr9:97987200-98015400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:97989400-98013400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:97990200-98013400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr9:97991200-98024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:97992600-98013400	Weak transcription	Liver	Liver
7	chr9:97994800-98017200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:97995400-98012800	Weak transcription	HSMM	muscle
9	chr9:97996800-98012800	Weak transcription	HSMMtube	muscle
10	chr9:97999800-98019000	Weak transcription	Aorta	Aorta
11	chr9:98002400-98015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:98005400-98013000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:98006000-98016800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:98007000-98013200	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:98007400-98024000	Weak transcription	Small Intestine	intestine
16	chr9:98009000-98018000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:98009000-98026600	Weak transcription	A549	lung
18	chr9:98009200-98013200	Weak transcription	Spleen	Spleen
19	chr9:98009200-98013200	Weak transcription	GM12878-XiMat	blood
20	chr9:98009200-98013600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:98009200-98014400	Weak transcription	Lung	lung
22	chr9:98009200-98016800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:98009200-98027600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:98009400-98014600	Weak transcription	Primary T cells from cord blood	blood
25	chr9:98009400-98019400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:98009600-98013200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:98009600-98016800	Weak transcription	Fetal Intestine Small	intestine
28	chr9:98009600-98023800	Weak transcription	Fetal Intestine Large	intestine
29	chr9:98011400-98013400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:98011600-98013400	Enhancers	Fetal Brain Female	brain
31	chr9:98012200-98013000	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr9:98012200-98013600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr9:98012200-98013600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:98012200-98013600	Enhancers	Fetal Kidney	kidney
35	chr9:98012400-98012800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr9:98012400-98013000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:98012400-98013000	Enhancers	HepG2	liver
38	chr9:98012400-98013200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:98012400-98013200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:98012400-98013200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr9:98012400-98013200	Enhancers	Colon Smooth Muscle	Colon
42	chr9:98012400-98013200	Enhancers	Esophagus	oesophagus
43	chr9:98012400-98013200	Enhancers	Fetal Thymus	thymus
44	chr9:98012400-98013200	Enhancers	Pancreas	Pancrea
45	chr9:98012400-98013200	Enhancers	Psoas Muscle	Psoas
46	chr9:98012400-98013200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr9:98012400-98013200	Enhancers	Stomach Mucosa	stomach
48	chr9:98012400-98013200	Enhancers	K562	blood
49	chr9:98012400-98013400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:98012400-98013400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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