Variant report

Variant	rs11078371
Chromosome Location	chr17:16996501-16996502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16990029..16991902-chr17:16996139..16998027,2	K562	blood:
2	chr17:16990609..16992779-chr17:16995614..16997816,2	MCF-7	breast:
3	chr17:16980742..16983360-chr17:16994783..16996638,2	K562	blood:

Variant related genes	Relation type
ENSG00000225442	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs1047799	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs1047805	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10852843	0.95[AMR][1000 genomes]
rs10852844	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10852845	0.95[AMR][1000 genomes]
rs10852846	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11078364	0.88[AMR][1000 genomes]
rs11078365	0.93[AMR][1000 genomes]
rs11078366	0.88[MEX][hapmap]
rs11078368	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078370	0.95[AMR][1000 genomes]
rs11078372	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078373	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078375	0.90[AMR][1000 genomes]
rs1110504	0.90[AMR][1000 genomes]
rs1110505	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11551189	0.85[ASN][1000 genomes]
rs11651460	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs11651938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11651988	0.95[AMR][1000 genomes]
rs11652079	0.90[AMR][1000 genomes]
rs11652678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11652756	0.95[AMR][1000 genomes]
rs11652936	0.95[AMR][1000 genomes]
rs11654247	0.90[AMR][1000 genomes]
rs11654360	0.90[AMR][1000 genomes]
rs11654562	0.93[AMR][1000 genomes]
rs11654887	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11657189	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11658084	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs11870035	0.87[ASN][1000 genomes]
rs11870483	0.96[ASN][1000 genomes]
rs12450109	0.95[AMR][1000 genomes]
rs12450213	0.93[AMR][1000 genomes]
rs12450238	0.93[AMR][1000 genomes]
rs12450467	0.95[AMR][1000 genomes]
rs12451054	0.95[AMR][1000 genomes]
rs12451343	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12452802	0.90[AMR][1000 genomes]
rs12601325	0.90[AMR][1000 genomes]
rs12601422	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12602129	0.95[AMR][1000 genomes]
rs12602583	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12602592	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12602839	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602867	0.90[AMR][1000 genomes]
rs12603417	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567815	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16961288	0.95[AMR][1000 genomes]
rs16961412	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs17794784	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs1877631	0.88[MEX][hapmap]
rs2292526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292530	0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs2349645	0.87[ASN][1000 genomes]
rs2349648	0.96[ASN][1000 genomes]
rs28452405	0.97[ASN][1000 genomes]
rs34001712	0.97[ASN][1000 genomes]
rs35650871	0.94[ASN][1000 genomes]
rs3744125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744127	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744131	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs3744132	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3744133	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs3744134	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[ASN][1000 genomes]
rs3744136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3744137	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs3744138	0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs3744139	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs3744140	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs3826305	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4073688	0.91[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4073940	0.81[MEX][hapmap]
rs4074611	0.95[AMR][1000 genomes]
rs4074612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074819	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4264448	0.95[AMR][1000 genomes]
rs4275916	0.95[AMR][1000 genomes]
rs4283273	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4321246	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4468683	0.88[ASN][1000 genomes]
rs4589617	0.81[ASN][1000 genomes]
rs4606773	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs4621033	0.95[AMR][1000 genomes]
rs4629023	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4641803	0.84[ASN][1000 genomes]
rs4985695	0.95[AMR][1000 genomes]
rs4985697	0.95[AMR][1000 genomes]
rs4985698	0.95[AMR][1000 genomes]
rs4985703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985704	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985714	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs4985716	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985719	0.95[AMR][1000 genomes]
rs4985721	0.97[ASN][1000 genomes]
rs4985727	0.95[AMR][1000 genomes]
rs4985728	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985730	0.96[ASN][1000 genomes]
rs4985737	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4985739	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs4985741	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs4985742	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985743	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4985744	0.90[AMR][1000 genomes]
rs4985747	0.86[AMR][1000 genomes]
rs55751545	0.90[AMR][1000 genomes]
rs56009207	0.95[AMR][1000 genomes]
rs56133536	0.87[ASN][1000 genomes]
rs57729820	0.96[ASN][1000 genomes]
rs57812549	0.88[AMR][1000 genomes]
rs58326998	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58472573	0.95[AMR][1000 genomes]
rs58814183	0.95[AMR][1000 genomes]
rs59394251	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60128647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61018209	0.90[AMR][1000 genomes]
rs61242604	0.91[ASN][1000 genomes]
rs7207187	0.95[AMR][1000 genomes]
rs7210339	0.95[AMR][1000 genomes]
rs7212275	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7214429	0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs7216677	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7217970	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs7218781	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap]
rs7223583	0.95[AMR][1000 genomes]
rs73979053	0.88[AMR][1000 genomes]
rs73979054	0.95[AMR][1000 genomes]
rs73979058	0.95[AMR][1000 genomes]
rs73979060	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979061	0.95[AMR][1000 genomes]
rs73979078	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979081	0.95[AMR][1000 genomes]
rs73979082	0.95[AMR][1000 genomes]
rs73979083	0.95[AMR][1000 genomes]
rs8064991	0.90[AMR][1000 genomes]
rs8066111	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8066234	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs8067563	0.95[AMR][1000 genomes]
rs8069259	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8071254	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8075751	0.88[MEX][hapmap]
rs8076273	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8077360	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9892695	0.85[ASN][1000 genomes]
rs9893676	0.85[ASN][1000 genomes]
rs9897510	0.85[ASN][1000 genomes]
rs9906028	0.94[ASN][1000 genomes]
rs9907109	0.96[ASN][1000 genomes]
rs9910857	0.87[ASN][1000 genomes]

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	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
2	nsv960194	chr17:16992376-17000025	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11078371	M-RIP	cis	multi-tissue	Pritchard
rs11078371	MPRIP	cis	lymphoblastoid	seeQTL
rs11078371	AK091337	cis	multi-tissue	Pritchard
rs11078371	PLD6	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16973600-16997600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr17:16978800-16996800	Strong transcription	Dnd41	blood
3	chr17:16985600-16996800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:16986800-16997600	Weak transcription	NHDF-Ad	bronchial
5	chr17:16986800-17013600	Weak transcription	HUVEC	blood vessel
6	chr17:16988000-16999800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:16988200-17000000	Weak transcription	Fetal Kidney	kidney
8	chr17:16988800-17000600	Weak transcription	Aorta	Aorta
9	chr17:16989600-16997400	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr17:16990400-16996600	Enhancers	Stomach Mucosa	stomach
11	chr17:16991000-17000200	Weak transcription	GM12878-XiMat	blood
12	chr17:16991400-16996600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:16991600-17000200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr17:16991800-16999000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr17:16992000-16996800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:16992000-16997400	Enhancers	Small Intestine	intestine
17	chr17:16992200-16999400	Weak transcription	NH-A	brain
18	chr17:16992200-16999600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr17:16992400-17000200	Weak transcription	Hela-S3	cervix
20	chr17:16992400-17010000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:16992600-16996800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr17:16992600-16997200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr17:16992600-17000000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr17:16992800-16999800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr17:16993000-17000600	Strong transcription	Primary T cells from cord blood	blood
26	chr17:16993200-16996600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr17:16993200-16997000	Weak transcription	K562	blood
28	chr17:16993200-17003800	Genic enhancers	Fetal Intestine Small	intestine
29	chr17:16993400-17000200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:16993400-17011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr17:16993800-16996800	Weak transcription	Brain Substantia Nigra	brain
32	chr17:16994200-16996600	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr17:16994400-16996600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:16994400-16999600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr17:16994600-16997600	Enhancers	Psoas Muscle	Psoas
36	chr17:16994600-16999200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr17:16994600-17003400	Enhancers	Ovary	ovary
38	chr17:16994600-17011600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr17:16994800-16996600	Enhancers	Right Atrium	heart
40	chr17:16994800-16996600	Strong transcription	NHEK	skin
41	chr17:16994800-16997400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr17:16994800-16999200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:16995000-16996600	Enhancers	Left Ventricle	heart
44	chr17:16995000-16997800	Enhancers	Colon Smooth Muscle	Colon
45	chr17:16995000-16997800	Enhancers	Fetal Lung	lung
46	chr17:16995000-16998200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr17:16995000-16998800	Weak transcription	Colonic Mucosa	Colon
48	chr17:16995000-16999400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr17:16995200-16996600	Weak transcription	NHLF	lung
50	chr17:16995200-16998000	Weak transcription	Fetal Thymus	thymus

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