Variant report

Variant	rs3738725
Chromosome Location	chr1:227174210-227174211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227165601..227167978-chr1:227173311..227176266,3	MCF-7	breast:
2	chr1:227154071..227157064-chr1:227173659..227175478,2	MCF-7	breast:
3	chr1:227173653..227176046-chr1:227186826..227189560,2	MCF-7	breast:
4	chr1:227173983..227176329-chr1:227192052..227193578,2	MCF-7	breast:
5	chr1:227168074..227172579-chr1:227173053..227177156,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1045252	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs1045285	0.89[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1045286	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045287	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1045289	0.87[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045290	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495273	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916075	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11577007	0.86[AMR][1000 genomes]
rs11578103	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11586604	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11587443	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11588904	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11589344	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1186	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12403236	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12406714	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12409230	0.83[AMR][1000 genomes]
rs12409428	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12409755	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12410103	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12593	0.91[MEX][hapmap];0.84[AMR][1000 genomes]
rs1343743	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1343744	0.82[AMR][1000 genomes]
rs17528667	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17592479	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600627	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17600669	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1929862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1929863	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1929864	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2183836	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2297412	0.86[ASN][1000 genomes]
rs2297415	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2297416	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2297418	0.96[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3738729	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3768419	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3768421	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768423	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768424	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768425	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795445	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3795446	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3795449	0.81[ASW][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3795451	0.81[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61834001	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61834004	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61834005	0.98[ASN][1000 genomes]
rs61834006	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6426558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426559	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6659424	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6664955	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6670924	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6684821	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6690803	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693535	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6699400	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6704144	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs68087483	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7520272	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7541033	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7549586	0.81[AMR][1000 genomes]
rs7552783	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9726097	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9727512	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3738725	CDC42BPA	cis	Artery Tibial	GTEx
rs3738725	ADCK3	cis	Whole Blood	GTEx
rs3738725	SERPINA7	trans	cerebellum	SCAN
rs3738725	CABC1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227147000-227177000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
4	chr1:227154800-227176800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:227158400-227174600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:227159000-227175800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:227160000-227174400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:227160000-227174400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:227160000-227174800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:227160000-227177200	Weak transcription	GM12878-XiMat	blood
12	chr1:227160600-227175600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:227160800-227181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:227162200-227176000	Strong transcription	Primary T cells from cord blood	blood
15	chr1:227162400-227175200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:227162400-227181600	Weak transcription	NHEK	skin
17	chr1:227162600-227175800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:227162600-227176600	Strong transcription	Thymus	Thymus
19	chr1:227163000-227180000	Weak transcription	HSMM	muscle
20	chr1:227163200-227175400	Strong transcription	Fetal Intestine Small	intestine
21	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:227163800-227176200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:227163800-227180400	Weak transcription	Fetal Brain Male	brain
24	chr1:227164200-227175800	Strong transcription	HepG2	liver
25	chr1:227164400-227175600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:227164600-227175000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:227164800-227175200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:227165000-227175000	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:227165000-227175400	Genic enhancers	Right Ventricle	heart
30	chr1:227165000-227176000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:227165200-227175000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:227165400-227175800	Strong transcription	Ovary	ovary
33	chr1:227166200-227174800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:227167000-227175200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:227168000-227174600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:227168800-227175400	Weak transcription	Psoas Muscle	Psoas
37	chr1:227168800-227175600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr1:227168800-227175600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
39	chr1:227169000-227175000	Strong transcription	Adipose Nuclei	Adipose
40	chr1:227169200-227175400	Strong transcription	Fetal Thymus	thymus
41	chr1:227169400-227175000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:227169400-227175200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:227169600-227175000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:227169600-227175000	Strong transcription	Gastric	stomach
45	chr1:227169600-227175800	Strong transcription	Liver	Liver
46	chr1:227169800-227175000	Strong transcription	Fetal Intestine Large	intestine
47	chr1:227169800-227175800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:227170000-227175000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:227170000-227176000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:227170200-227175400	Strong transcription	Colon Smooth Muscle	Colon

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