Variant report

Variant	rs9995068
Chromosome Location	chr4:47580015-47580016
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr4:47579778-47580305	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr4:47579781-47580360	HUVEC	blood vessel:	n/a	n/a
3	FOS	chr4:47579881-47580308	HUVEC	blood vessel:	n/a	n/a
4	STAT3	chr4:47579987-47580187	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ATP10D	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10003620	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10006939	0.97[ASN][1000 genomes]
rs10017276	0.81[ASW][hapmap];0.84[LWK][hapmap]
rs10034504	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10938490	0.80[CHD][hapmap];0.80[ASN][1000 genomes]
rs10938491	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs10938492	0.96[ASN][1000 genomes]
rs10938493	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs11723676	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs11728366	0.97[ASN][1000 genomes]
rs11728642	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs11729212	0.97[ASN][1000 genomes]
rs11729247	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs11729252	1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs11730590	0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs12498466	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs12500474	0.97[ASN][1000 genomes]
rs12502166	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs12502321	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs12502323	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs12507138	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs12507737	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs12507939	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs13101892	0.81[ASW][hapmap]
rs13105858	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs13106043	0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs13110314	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13122990	0.97[ASN][1000 genomes]
rs13123471	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs13123704	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs13125264	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs13134125	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs13151340	0.97[ASN][1000 genomes]
rs1344122	0.81[ASW][hapmap]
rs16851681	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[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28414421	0.97[ASN][1000 genomes]
rs28535313	0.97[ASN][1000 genomes]
rs34442412	0.97[ASN][1000 genomes]
rs34707051	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34872589	0.97[ASN][1000 genomes]
rs3922408	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs3924898	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs3924899	0.97[ASN][1000 genomes]
rs3924900	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs4298115	0.81[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs4391005	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4694857	0.81[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs6810449	0.92[ASN][1000 genomes]
rs6811048	0.97[ASN][1000 genomes]
rs6823365	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs6825063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827604	0.81[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs6829677	0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs6832417	0.97[ASN][1000 genomes]
rs6840205	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6842577	0.97[ASN][1000 genomes]
rs6843438	0.97[ASN][1000 genomes]
rs6851221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657209	0.81[ASW][hapmap]
rs7686393	0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs7687166	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs7695942	1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs7699738	0.81[ASW][hapmap]
rs9998849	0.81[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829923	chr4:47436139-47678443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9995068	GABRA2	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47534600-47580800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:47534600-47592000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr4:47539600-47589000	Weak transcription	Colonic Mucosa	Colon
4	chr4:47546400-47589400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:47548800-47583800	Weak transcription	Psoas Muscle	Psoas
6	chr4:47555800-47594800	Weak transcription	Stomach Mucosa	stomach
7	chr4:47556400-47588000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:47564000-47589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:47564600-47580800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:47567600-47585000	Weak transcription	NHDF-Ad	bronchial
11	chr4:47567600-47588400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:47567600-47598400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:47567800-47590800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:47568000-47592000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr4:47568200-47592200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:47568200-47595800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:47569800-47582000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:47569800-47589400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:47570000-47592200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr4:47570200-47581800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:47570200-47592200	Strong transcription	Primary B cells from cord blood	blood
22	chr4:47570400-47591800	Strong transcription	Dnd41	blood
23	chr4:47570400-47595400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr4:47570600-47592000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:47570800-47580800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:47570800-47582800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:47570800-47586200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:47570800-47595800	Strong transcription	Osteobl	bone
29	chr4:47570800-47596000	Strong transcription	Placenta	Placenta
30	chr4:47571000-47591800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:47571200-47581600	Strong transcription	Liver	Liver
32	chr4:47572000-47584000	Weak transcription	NHLF	lung
33	chr4:47572000-47588000	Weak transcription	Right Ventricle	heart
34	chr4:47572200-47583800	Weak transcription	Brain Angular Gyrus	brain
35	chr4:47573400-47593600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:47573800-47591000	Weak transcription	Brain Germinal Matrix	brain
37	chr4:47574200-47581000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr4:47574400-47587800	Weak transcription	Brain Substantia Nigra	brain
39	chr4:47574400-47595000	Weak transcription	Fetal Brain Female	brain
40	chr4:47575000-47610200	Weak transcription	Fetal Brain Male	brain
41	chr4:47575200-47580200	Weak transcription	Lung	lung
42	chr4:47575200-47580600	Weak transcription	Esophagus	oesophagus
43	chr4:47575200-47583800	Weak transcription	Gastric	stomach
44	chr4:47575200-47588400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:47575200-47588600	Weak transcription	Fetal Heart	heart
46	chr4:47575200-47589000	Weak transcription	Spleen	Spleen
47	chr4:47575200-47589600	Weak transcription	Pancreas	Pancrea
48	chr4:47575200-47592400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr4:47575400-47583800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:47575600-47583800	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links