Variant report

Variant	rs9369454
Chromosome Location	chr6:44087665-44087666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44076515..44082841-chr6:44082960..44087705,9	MCF-7	breast:
2	chr6:43594914..43597749-chr6:44087442..44089146,2	K562	blood:
3	chr6:44086896..44089729-chr6:44217507..44220003,2	K562	blood:
4	chr6:44086295..44088252-chr6:44102211..44103755,2	MCF-7	breast:
5	chr6:44072715..44074361-chr6:44086562..44088391,2	K562	blood:

Variant related genes	Relation type
ENSG00000137216	Chromatin interaction
ENSG00000172432	Chromatin interaction
ENSG00000124688	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10948121	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12191873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12199128	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12202501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206251	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12206795	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064639	1.00[AFR][1000 genomes]
rs2064640	1.00[AFR][1000 genomes]
rs2092870	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236061	1.00[AFR][1000 genomes]
rs3734695	0.87[JPT][hapmap]
rs3734696	0.97[EUR][1000 genomes]
rs3734697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4628095	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711764	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711766	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4714738	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4714750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714761	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs4714762	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62401766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62403189	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs729391	1.00[ASW][hapmap]
rs833805	1.00[ASW][hapmap]
rs877112	0.94[JPT][hapmap]
rs9349270	1.00[AFR][1000 genomes]
rs9349271	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349272	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369448	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369449	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369450	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369456	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369457	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9369458	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs9369459	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9381287	1.00[AFR][1000 genomes]
rs9381294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9394984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS 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	201 gene(s)	inside rSNPs	diseases
2	nsv462935	chr6:44046143-44117607	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv603002	chr6:44046143-44117607	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44058800-44093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:44066000-44091000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:44081800-44093600	Weak transcription	Brain Substantia Nigra	brain
4	chr6:44082000-44088800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:44082000-44090800	Weak transcription	Spleen	Spleen
6	chr6:44082200-44087800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:44082200-44087800	Weak transcription	Primary B cells from cord blood	blood
8	chr6:44082200-44093600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:44082400-44087800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:44082400-44088000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:44082400-44090400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:44082800-44089400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:44083200-44093800	Weak transcription	Fetal Brain Male	brain
14	chr6:44083400-44090400	Weak transcription	Fetal Kidney	kidney
15	chr6:44083600-44090400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:44083600-44090800	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:44083600-44092600	Enhancers	HMEC	breast
18	chr6:44083800-44087800	Weak transcription	Lung	lung
19	chr6:44083800-44088400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:44083800-44090400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:44083800-44093800	Enhancers	Stomach Mucosa	stomach
22	chr6:44084000-44087800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:44084000-44088600	Enhancers	Pancreas	Pancrea
24	chr6:44084000-44093800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr6:44084200-44087800	Weak transcription	Fetal Brain Female	brain
26	chr6:44084200-44088400	Weak transcription	Brain Germinal Matrix	brain
27	chr6:44084200-44088600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:44084200-44088600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:44084400-44087800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:44084400-44088000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:44084400-44090400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:44084600-44088400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:44084600-44088600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:44084600-44088800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:44084800-44089200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:44085000-44090400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:44085200-44087800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:44085200-44088200	Enhancers	NHDF-Ad	bronchial
39	chr6:44085200-44088400	Enhancers	Psoas Muscle	Psoas
40	chr6:44085200-44088600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:44085200-44092800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:44085400-44089200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:44085400-44089800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr6:44085600-44088000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:44085800-44087800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr6:44085800-44093800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:44086000-44088800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:44086000-44088800	Weak transcription	Fetal Intestine Large	intestine
49	chr6:44086000-44089200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:44086200-44088200	Enhancers	HepG2	liver

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