Variant report

Variant	rs4073940
Chromosome Location	chr17:16977810-16977811
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16973848..16977843-chr17:17007115..17009088,3	K562	blood:
2	chr17:16973117..16976449-chr17:16977265..16979682,3	MCF-7	breast:
3	chr17:16972185..16973700-chr17:16976776..16979129,2	MCF-7	breast:
4	chr17:16944012..16948651-chr17:16974298..16979165,8	MCF-7	breast:
5	chr17:16971774..16974202-chr17:16976172..16978952,3	K562	blood:
6	chr17:16975491..16978124-chr17:16978720..16981255,2	K562	blood:

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction
ENSG00000225442	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10852843	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852845	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11078364	0.81[ASN][1000 genomes]
rs11078365	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11078366	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11078370	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078371	0.81[MEX][hapmap]
rs11078373	0.81[MEX][hapmap]
rs11078375	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11651460	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs11651988	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11652674	0.81[EUR][1000 genomes]
rs11652756	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652936	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654247	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs11654360	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11654562	0.89[CHB][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11654887	0.86[AMR][1000 genomes]
rs11657189	0.86[AMR][1000 genomes]
rs11658084	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11658904	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12450109	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12450213	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12450238	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12450467	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451054	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451343	0.96[AMR][1000 genomes]
rs12452303	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12601325	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12602124	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602129	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602583	0.80[AMR][1000 genomes]
rs12602592	0.86[AMR][1000 genomes]
rs12602839	0.94[AMR][1000 genomes]
rs12602867	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1567815	0.86[AMR][1000 genomes]
rs16961288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16961412	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]
rs1877631	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs3744132	0.81[MEX][hapmap]
rs3744133	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs3744140	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4073688	0.94[MEX][hapmap]
rs4074611	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264448	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275916	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4606773	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621033	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629023	1.00[MEX][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes]
rs4985695	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985697	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985698	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985704	0.94[MEX][hapmap];0.86[AMR][1000 genomes]
rs4985712	0.85[ASN][1000 genomes]
rs4985714	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985716	0.96[AMR][1000 genomes]
rs4985719	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985723	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985727	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985737	0.86[AMR][1000 genomes]
rs4985739	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs4985742	0.94[MEX][hapmap];0.86[AMR][1000 genomes]
rs4985743	0.86[AMR][1000 genomes]
rs55751545	0.81[EUR][1000 genomes]
rs56009207	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58472573	1.00[ASN][1000 genomes]
rs58814183	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7207187	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7210339	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212275	0.96[AMR][1000 genomes]
rs7216677	0.86[AMR][1000 genomes]
rs7217970	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs7223583	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7223686	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs7223924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73979053	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73979054	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73979058	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73979061	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979081	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979082	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979083	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064991	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8067563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069259	0.86[AMR][1000 genomes]
rs8071254	0.96[AMR][1000 genomes]
rs8075751	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8077360	0.86[AMR][1000 genomes]
rs9910011	0.85[ASN][1000 genomes]

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	nsv1059280	chr17:16975059-17017957	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4073940	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16952600-16996400	Weak transcription	Fetal Brain Male	brain
2	chr17:16954800-16981200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr17:16955400-16981200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:16959200-16982200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:16959600-16979800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr17:16959600-16992000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:16966200-16980800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr17:16970000-16981000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr17:16970800-16980400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:16971000-16979000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr17:16973000-16981000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:16973000-16981200	Enhancers	Brain Anterior Caudate	brain
13	chr17:16973200-16985000	Genic enhancers	A549	lung
14	chr17:16973400-16981400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:16973600-16979800	Genic enhancers	HSMM	muscle
16	chr17:16973600-16980000	Genic enhancers	HMEC	breast
17	chr17:16973600-16997600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr17:16973800-16978200	Enhancers	Stomach Mucosa	stomach
19	chr17:16973800-16978200	Weak transcription	GM12878-XiMat	blood
20	chr17:16973800-16982200	Strong transcription	Fetal Brain Female	brain
21	chr17:16974000-16995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr17:16974200-16978000	Genic enhancers	Spleen	Spleen
23	chr17:16974200-16978200	Genic enhancers	Gastric	stomach
24	chr17:16974200-16978200	Genic enhancers	Right Ventricle	heart
25	chr17:16974200-16979200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:16974200-16979400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:16974200-16979600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr17:16974200-16979600	Enhancers	Psoas Muscle	Psoas
29	chr17:16974200-16979800	Enhancers	Right Atrium	heart
30	chr17:16974200-16980000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr17:16974200-16980600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr17:16974200-16981200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr17:16974200-16981800	Genic enhancers	Fetal Intestine Large	intestine
34	chr17:16974200-16985200	Enhancers	Brain Angular Gyrus	brain
35	chr17:16974400-16979600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:16974400-16979800	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr17:16974400-16985200	Genic enhancers	Fetal Intestine Small	intestine
38	chr17:16974600-16978000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr17:16974600-16978400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr17:16974600-16979000	Enhancers	Fetal Thymus	thymus
41	chr17:16974800-16978600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr17:16975200-16978400	Genic enhancers	Esophagus	oesophagus
43	chr17:16975200-16979200	Enhancers	Fetal Heart	heart
44	chr17:16975200-16979400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr17:16975200-16979400	Enhancers	Left Ventricle	heart
46	chr17:16975200-16979600	Genic enhancers	Placenta	Placenta
47	chr17:16975200-16979800	Genic enhancers	Fetal Stomach	stomach
48	chr17:16975400-16979400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr17:16975400-16980400	Weak transcription	HepG2	liver
50	chr17:16975600-16978000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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