Variant report

Variant	rs2245808
Chromosome Location	chr4:8418430-8418431
allele	A/G
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	POLR2A	chr4:8418332-8418553	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8416707..8419298-chr4:8428396..8430193,3	MCF-7	breast:

Variant related genes	Relation type
ACOX3	TF binding region
ENSG00000087008	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11729265	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12503034	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880025	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2002860	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049302	0.99[ASN][1000 genomes]
rs2140336	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2245515	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245809	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386223	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2631724	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2631727	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631728	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631729	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631730	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631733	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631737	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631750	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2631752	0.92[ASN][1000 genomes]
rs2631757	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2631763	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2631764	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631765	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2631766	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631767	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2631769	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688221	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688228	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688229	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688234	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688239	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2688240	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2688244	0.96[ASN][1000 genomes]
rs2688246	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3103090	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3103098	0.86[JPT][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes]
rs3115396	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3775893	0.89[EUR][1000 genomes]
rs4325994	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56343159	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs954270	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs954271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv593639	chr4:8394376-8424108	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2245808	ACOX3	cis	parietal	SCAN
rs2245808	ACOX3	cis	lymphoblastoid	seeQTL
rs2245808	C4orf23	cis	cerebellum	SCAN
rs2245808	TBC1D14	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8383800-8419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:8384800-8418600	Strong transcription	Primary T cells from cord blood	blood
3	chr4:8396600-8419400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:8397600-8420400	Weak transcription	NHDF-Ad	bronchial
5	chr4:8399600-8429400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:8403200-8419400	Strong transcription	Fetal Intestine Small	intestine
7	chr4:8404600-8429400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:8404800-8420600	Weak transcription	Psoas Muscle	Psoas
9	chr4:8405600-8418600	Strong transcription	Liver	Liver
10	chr4:8405600-8418800	Strong transcription	Aorta	Aorta
11	chr4:8406600-8418800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:8407800-8419200	Weak transcription	Fetal Thymus	thymus
13	chr4:8408800-8422400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:8410400-8418600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:8411000-8419000	Strong transcription	Pancreas	Pancrea
16	chr4:8411800-8418800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:8412400-8418800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:8412400-8421000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:8412800-8418600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:8412800-8418600	Strong transcription	Brain Germinal Matrix	brain
21	chr4:8412800-8418600	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:8412800-8418800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr4:8412800-8418800	Strong transcription	Spleen	Spleen
24	chr4:8412800-8420600	Weak transcription	K562	blood
25	chr4:8412800-8425600	Weak transcription	Fetal Heart	heart
26	chr4:8413000-8418600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:8413000-8418600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:8413000-8418800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:8413000-8419000	Strong transcription	Fetal Brain Female	brain
30	chr4:8413000-8419200	Strong transcription	Fetal Intestine Large	intestine
31	chr4:8413000-8419400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:8413000-8419400	Strong transcription	Fetal Stomach	stomach
33	chr4:8413000-8423400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:8413400-8418600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:8413400-8418800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:8413600-8418800	Strong transcription	Brain Cingulate Gyrus	brain
37	chr4:8413600-8418800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr4:8414800-8418800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:8415200-8418600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:8415200-8419000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:8415400-8418600	Strong transcription	Brain Angular Gyrus	brain
42	chr4:8415600-8419400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:8416400-8421400	Weak transcription	HSMM	muscle
44	chr4:8416400-8428000	Weak transcription	Fetal Brain Male	brain
45	chr4:8416800-8419200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:8416800-8421200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:8416800-8421400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr4:8416800-8429000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:8416800-8429000	Weak transcription	Brain Substantia Nigra	brain
50	chr4:8416800-8429000	Weak transcription	Fetal Kidney	kidney

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