Variant report

Variant	rs11651460
Chromosome Location	chr17:17051974-17051975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17050223..17052040-chr17:17108443..17111394,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1047805	0.95[AMR][1000 genomes]
rs10852843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10852844	0.90[AMR][1000 genomes]
rs10852845	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10852846	0.95[AMR][1000 genomes]
rs11078364	0.88[AMR][1000 genomes]
rs11078365	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11078366	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[MEX][hapmap]
rs11078370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11078371	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs11078372	0.90[AMR][1000 genomes]
rs11078373	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs11078375	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1110504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1110505	0.95[AMR][1000 genomes]
rs11651938	0.95[AMR][1000 genomes]
rs11651988	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11652079	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11652674	1.00[EUR][1000 genomes]
rs11652678	0.95[AMR][1000 genomes]
rs11652756	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11652936	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11654247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654360	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11654562	0.90[CHB][hapmap];0.93[AMR][1000 genomes]
rs11658084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11658904	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs12450109	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12450213	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12450238	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12450467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12451054	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12452119	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12452303	0.81[EUR][1000 genomes]
rs12452802	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12602124	0.81[EUR][1000 genomes]
rs12602129	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12602867	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16961288	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16961412	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1877631	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs2292526	0.91[AMR][1000 genomes]
rs3744125	0.95[AMR][1000 genomes]
rs3744127	0.95[AMR][1000 genomes]
rs3744132	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs3744133	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744136	0.95[AMR][1000 genomes]
rs3744140	0.82[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826305	0.93[AMR][1000 genomes]
rs4073940	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]
rs4074611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4074612	0.90[AMR][1000 genomes]
rs4074819	0.95[AMR][1000 genomes]
rs4264448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4275916	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4283273	0.95[AMR][1000 genomes]
rs4321246	0.91[AMR][1000 genomes]
rs4606773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4621033	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4629023	0.82[MEX][hapmap]
rs4985695	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4985697	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4985698	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985703	0.95[AMR][1000 genomes]
rs4985704	0.81[MEX][hapmap]
rs4985714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4985715	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4985719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4985727	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4985739	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];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985742	0.88[MEX][hapmap]
rs4985744	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985747	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55751545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56009207	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57812549	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58326998	0.95[AMR][1000 genomes]
rs58472573	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs58814183	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59394251	0.95[AMR][1000 genomes]
rs60128647	0.90[AMR][1000 genomes]
rs61018209	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7207187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7210339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7217970	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];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7223583	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7223686	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs7223924	0.81[EUR][1000 genomes]
rs73979053	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73979054	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73979058	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73979060	0.90[AMR][1000 genomes]
rs73979061	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73979081	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73979082	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73979083	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8064991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8066111	0.95[AMR][1000 genomes]
rs8067563	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8075751	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[MEX][hapmap]
rs9894565	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv524958	chr17:17029718-17060805	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11651460	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17029800-17088400	Strong transcription	Dnd41	blood
2	chr17:17030000-17052200	Strong transcription	Primary B cells from peripheral blood	blood
3	chr17:17030000-17088000	Strong transcription	Duodenum Mucosa	Duodenum
4	chr17:17030200-17055000	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr17:17030400-17055800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr17:17030400-17059800	Strong transcription	Fetal Intestine Small	intestine
7	chr17:17030400-17079200	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
9	chr17:17031000-17078800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr17:17031200-17057200	Strong transcription	Primary T cells from cord blood	blood
11	chr17:17031200-17067800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr17:17032000-17055000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr17:17032000-17073800	Strong transcription	Fetal Lung	lung
14	chr17:17032200-17073600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:17034800-17072800	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr17:17037200-17074200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:17038400-17093800	Strong transcription	Fetal Brain Female	brain
18	chr17:17038800-17058400	Weak transcription	Fetal Brain Male	brain
19	chr17:17041400-17054200	Strong transcription	Hela-S3	cervix
20	chr17:17043000-17055200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr17:17044000-17052800	Strong transcription	HSMMtube	muscle
22	chr17:17044200-17053400	Strong transcription	NHLF	lung
23	chr17:17044200-17083600	Strong transcription	Thymus	Thymus
24	chr17:17044600-17052200	Weak transcription	HepG2	liver
25	chr17:17044600-17053800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:17044600-17054800	Strong transcription	Liver	Liver
27	chr17:17044800-17053400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:17044800-17054600	Strong transcription	Adipose Nuclei	Adipose
29	chr17:17045000-17054600	Strong transcription	Placenta	Placenta
30	chr17:17045000-17088400	Strong transcription	Brain Germinal Matrix	brain
31	chr17:17045200-17052000	Strong transcription	A549	lung
32	chr17:17045200-17052200	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr17:17045200-17054000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:17045200-17055800	Strong transcription	Fetal Thymus	thymus
35	chr17:17045200-17071600	Strong transcription	Primary B cells from cord blood	blood
36	chr17:17045200-17075600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr17:17045200-17093800	Strong transcription	Fetal Stomach	stomach
38	chr17:17045400-17052200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:17045600-17053600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr17:17045600-17054600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr17:17045600-17071000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr17:17045600-17072800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:17045800-17053400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:17045800-17053800	Strong transcription	Esophagus	oesophagus
45	chr17:17045800-17055000	Strong transcription	Ovary	ovary
46	chr17:17045800-17059200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr17:17045800-17065600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr17:17046000-17052000	Strong transcription	NHEK	skin
49	chr17:17046000-17054800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr17:17046000-17059800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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