Variant report

Variant	rs400727
Chromosome Location	chr9:97936269-97936270
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	chr9:97933130..97934889-chr9:97935078..97937126,2	MCF-7	breast:
2	chr9:97935732..97938489-chr9:97958539..97960476,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238746	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12683182	0.85[JPT][hapmap]
rs12686588	0.85[JPT][hapmap]
rs1623009	1.00[EUR][1000 genomes]
rs173339	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1875835	0.86[JPT][hapmap]
rs2061799	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2404458	0.85[JPT][hapmap]
rs242448	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2655055	1.00[EUR][1000 genomes]
rs2765817	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs356660	1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356661	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs356662	1.00[EUR][1000 genomes]
rs356663	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs356671	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs356685	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356686	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3780560	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3780566	0.85[JPT][hapmap]
rs420089	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4647352	0.86[JPT][hapmap]
rs4647354	0.85[JPT][hapmap]
rs4647360	0.86[JPT][hapmap]
rs4647367	0.86[JPT][hapmap]
rs4647378	0.86[JPT][hapmap]
rs4647387	0.86[JPT][hapmap]
rs4647397	0.86[JPT][hapmap]
rs4647402	0.85[JPT][hapmap]
rs4647408	0.85[JPT][hapmap]
rs4647414	0.85[JPT][hapmap]
rs4647436	0.86[JPT][hapmap]
rs4647437	0.86[JPT][hapmap]
rs4647466	0.85[JPT][hapmap]
rs4647472	0.86[JPT][hapmap]
rs4647473	0.85[JPT][hapmap]
rs4647484	0.85[JPT][hapmap]
rs4647491	0.86[JPT][hapmap]
rs4647493	0.85[JPT][hapmap]
rs4647509	0.85[JPT][hapmap]
rs4647514	0.85[JPT][hapmap]
rs4647516	0.85[JPT][hapmap]
rs4743989	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4744437	0.90[CEU][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs4744440	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs475413	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs607105	0.92[EUR][1000 genomes]
rs6479596	0.88[JPT][hapmap]
rs6479597	0.88[JPT][hapmap]
rs648615	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs651009	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[EUR][1000 genomes]
rs7022739	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs7854840	0.86[JPT][hapmap]
rs9299427	0.89[EUR][1000 genomes]
rs9792415	0.85[JPT][hapmap]
rs9792533	0.85[JPT][hapmap]

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	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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97893800-97940400	Weak transcription	Pancreas	Pancrea
2	chr9:97906600-97950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:97920000-97952000	Weak transcription	Aorta	Aorta
4	chr9:97920000-97952000	Weak transcription	Esophagus	oesophagus
5	chr9:97920400-97951800	Weak transcription	HepG2	liver
6	chr9:97925800-97938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:97925800-97944800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr9:97926000-97937800	Weak transcription	Psoas Muscle	Psoas
9	chr9:97927600-97950400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:97930000-97945200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:97930000-97945400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:97930600-97939400	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:97930600-97943400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:97930600-97944800	Weak transcription	Lung	lung
15	chr9:97930600-97950400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:97930600-97950800	Weak transcription	Thymus	Thymus
17	chr9:97930600-97952000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:97930800-97940400	Weak transcription	Fetal Thymus	thymus
19	chr9:97930800-97941600	Weak transcription	Liver	Liver
20	chr9:97930800-97951600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr9:97930800-97952400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:97931200-97937800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:97931200-97940000	Weak transcription	Fetal Intestine Small	intestine
24	chr9:97931800-97937800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:97932200-97944800	Weak transcription	Primary T cells from cord blood	blood
26	chr9:97932200-97945000	Weak transcription	Fetal Intestine Large	intestine
27	chr9:97933200-97950600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr9:97933400-97938000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:97933400-97945400	Weak transcription	Fetal Kidney	kidney
30	chr9:97933600-97937000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr9:97933600-97938800	Weak transcription	Hela-S3	cervix
32	chr9:97933600-97944200	Weak transcription	Fetal Stomach	stomach
33	chr9:97933800-97938000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:97933800-97938200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:97933800-97939400	Weak transcription	Fetal Lung	lung
36	chr9:97934200-97937800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr9:97934200-97937800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr9:97934200-97937800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:97934200-97937800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr9:97934400-97936600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:97935000-97937200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr9:97935400-97937800	Enhancers	Fetal Heart	heart

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