Variant report

Variant	rs28452405
Chromosome Location	chr17:16982589-16982590
allele	C/T
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	NR3C1	chr17:16982541-16982941	A549	lung:	n/a	chr17:16982739-16982753
2	NR3C1	chr17:16982331-16983077	A549	lung:	n/a	chr17:16982739-16982753
3	NR3C1	chr17:16982465-16983020	A549	lung:	n/a	chr17:16982739-16982753
4	NR3C1	chr17:16982494-16983000	A549	lung:	n/a	chr17:16982739-16982753

No.	Distal block	Cell Line	Cell type
1	chr17:16944416..16947050-chr17:16979219..16983384,3	MCF-7	breast:
2	chr17:16978185..16979772-chr17:16981297..16982977,2	MCF-7	breast:
3	chr17:16920470..16922796-chr17:16981423..16984163,2	MCF-7	breast:
4	chr17:16784922..16787392-chr17:16982105..16984669,2	K562	blood:

Variant related genes	Relation type
MPRIP-AS1	TF binding region
ENSG00000133030	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1047799	0.82[AMR][1000 genomes]
rs10852844	0.96[ASN][1000 genomes]
rs10852846	0.85[ASN][1000 genomes]
rs11078368	0.97[ASN][1000 genomes]
rs11078371	0.97[ASN][1000 genomes]
rs11078372	0.96[ASN][1000 genomes]
rs11078373	0.86[ASN][1000 genomes]
rs1110505	0.82[ASN][1000 genomes]
rs11551189	0.87[ASN][1000 genomes]
rs11651938	0.86[ASN][1000 genomes]
rs11652678	0.86[ASN][1000 genomes]
rs11654887	0.85[ASN][1000 genomes]
rs11870035	0.89[ASN][1000 genomes]
rs11870422	0.81[ASN][1000 genomes]
rs11870483	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11870997	0.81[ASN][1000 genomes]
rs12451343	0.96[ASN][1000 genomes]
rs12601422	0.81[ASN][1000 genomes]
rs12602839	0.97[ASN][1000 genomes]
rs12603417	0.97[ASN][1000 genomes]
rs1567815	0.82[ASN][1000 genomes]
rs17794784	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2292526	0.86[ASN][1000 genomes]
rs2292530	0.84[ASN][1000 genomes]
rs2349645	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2349648	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34001712	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34976658	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35650871	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3744131	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3744132	0.84[ASN][1000 genomes]
rs3744134	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3744136	0.86[ASN][1000 genomes]
rs3744137	0.89[ASN][1000 genomes]
rs3744138	0.89[ASN][1000 genomes]
rs3744139	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4073688	0.94[ASN][1000 genomes]
rs4074612	0.97[ASN][1000 genomes]
rs4074819	0.86[ASN][1000 genomes]
rs4321246	0.86[ASN][1000 genomes]
rs4468683	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4629023	0.97[ASN][1000 genomes]
rs4641803	0.82[ASN][1000 genomes]
rs4985703	0.86[ASN][1000 genomes]
rs4985704	0.85[ASN][1000 genomes]
rs4985716	0.94[ASN][1000 genomes]
rs4985721	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4985728	0.97[ASN][1000 genomes]
rs4985730	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4985737	0.86[ASN][1000 genomes]
rs4985741	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985745	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56133536	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57729820	0.93[ASN][1000 genomes]
rs58326998	0.85[ASN][1000 genomes]
rs59394251	0.85[ASN][1000 genomes]
rs60128647	0.97[ASN][1000 genomes]
rs61242604	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7211576	0.81[ASN][1000 genomes]
rs7212275	0.92[ASN][1000 genomes]
rs7214429	0.87[ASN][1000 genomes]
rs7216677	0.86[ASN][1000 genomes]
rs73979060	0.97[ASN][1000 genomes]
rs73979078	0.97[ASN][1000 genomes]
rs8066111	0.83[ASN][1000 genomes]
rs8066234	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8069259	0.86[ASN][1000 genomes]
rs8071254	0.93[ASN][1000 genomes]
rs8076273	0.83[ASN][1000 genomes]
rs8077360	0.86[ASN][1000 genomes]
rs9892695	0.83[ASN][1000 genomes]
rs9893676	0.87[ASN][1000 genomes]
rs9897510	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9906028	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9907109	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9910857	0.83[EUR][1000 genomes];0.89[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
rs28452405	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr17:16959600-16992000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr17:16973200-16985000	Genic enhancers	A549	lung
4	chr17:16973600-16997600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:16974000-16995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:16974200-16985200	Enhancers	Brain Angular Gyrus	brain
7	chr17:16974400-16985200	Genic enhancers	Fetal Intestine Small	intestine
8	chr17:16975800-16984600	Strong transcription	Primary B cells from cord blood	blood
9	chr17:16977200-16991200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr17:16977400-16992400	Strong transcription	Hela-S3	cervix
11	chr17:16978200-16982600	Strong transcription	GM12878-XiMat	blood
12	chr17:16978600-16984200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:16978600-16984600	Genic enhancers	Gastric	stomach
14	chr17:16978600-16991000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:16978800-16986400	Genic enhancers	Fetal Muscle Leg	muscle
16	chr17:16978800-16996800	Strong transcription	Dnd41	blood
17	chr17:16979000-16983800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr17:16979000-16984800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr17:16979000-16988600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr17:16979000-16989000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:16979200-16982600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:16979200-16982600	Strong transcription	Brain Germinal Matrix	brain
23	chr17:16979200-16984000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr17:16979200-16991400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr17:16979400-16982600	Strong transcription	Osteobl	bone
26	chr17:16979400-16982800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:16979400-16984200	Genic enhancers	Lung	lung
28	chr17:16979400-16990000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:16979400-16991200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr17:16979400-16991400	Strong transcription	Primary T cells from cord blood	blood
31	chr17:16979600-16982800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr17:16979600-16985000	Genic enhancers	Rectal Mucosa Donor 29	rectum
33	chr17:16979600-16985000	Genic enhancers	Stomach Smooth Muscle	stomach
34	chr17:16979600-16986000	Weak transcription	HUVEC	blood vessel
35	chr17:16979600-16989000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr17:16979600-16989400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr17:16979800-16982600	Strong transcription	Fetal Stomach	stomach
38	chr17:16979800-16983000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:16979800-16984400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr17:16979800-16992200	Strong transcription	Thymus	Thymus
41	chr17:16980000-16983400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr17:16980000-16984200	Strong transcription	Fetal Thymus	thymus
43	chr17:16980200-16982600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:16980200-16983000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr17:16980200-16985000	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr17:16980400-16982800	Genic enhancers	Rectal Mucosa Donor 31	rectum
47	chr17:16980400-16983200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr17:16980600-16983400	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr17:16980600-16984000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr17:16980600-16984000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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