Variant report

Variant	rs17093729
Chromosome Location	chr14:71552352-71552353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP3K9-9	chr14:71552199-71552550	NONHSAT037605

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10137675	0.83[ASN][1000 genomes]
rs10142792	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10147124	0.88[ASN][1000 genomes]
rs10162428	0.86[ASN][1000 genomes]
rs10220379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10483835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11846003	0.85[ASN][1000 genomes]
rs11847244	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs11849831	0.85[ASN][1000 genomes]
rs12432180	0.90[ASN][1000 genomes]
rs12432587	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12433409	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12435253	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12436649	0.81[ASN][1000 genomes]
rs12436920	0.87[ASN][1000 genomes]
rs12436970	0.87[ASN][1000 genomes]
rs12436976	0.87[ASN][1000 genomes]
rs12880918	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];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12881674	0.83[CHB][hapmap];0.86[CHD][hapmap];0.89[MEX][hapmap]
rs12891140	0.81[AMR][1000 genomes]
rs12891445	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12895177	0.86[ASN][1000 genomes]
rs12896855	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108711	0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs17108730	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17108753	0.86[ASN][1000 genomes]
rs17108755	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17108869	0.92[ASN][1000 genomes]
rs17108873	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17108897	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17109008	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1978163	0.87[ASN][1000 genomes]
rs2051865	0.88[ASN][1000 genomes]
rs2158998	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2286312	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[ASN][1000 genomes]
rs2286314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2526891	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34007279	0.81[ASN][1000 genomes]
rs34119685	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34740221	0.88[ASN][1000 genomes]
rs34785361	0.83[ASN][1000 genomes]
rs34927411	0.88[ASN][1000 genomes]
rs34968850	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34971726	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34998980	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35041597	0.86[ASN][1000 genomes]
rs35092982	0.86[ASN][1000 genomes]
rs35127721	0.84[ASN][1000 genomes]
rs35168506	0.86[ASN][1000 genomes]
rs35523654	0.94[ASN][1000 genomes]
rs35714454	0.94[ASN][1000 genomes]
rs35725944	0.88[ASN][1000 genomes]
rs36089307	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4488390	0.88[ASN][1000 genomes]
rs4614662	0.87[ASN][1000 genomes]
rs4902872	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4902873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902874	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902877	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4902878	0.92[ASN][1000 genomes]
rs4902882	0.89[ASN][1000 genomes]
rs4902883	0.87[ASN][1000 genomes]
rs4902884	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs61990447	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71425229	0.86[ASN][1000 genomes]
rs71425386	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7146777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7147788	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs7148530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7152435	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7157279	0.81[ASN][1000 genomes]
rs7158548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73297555	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7492431	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8010701	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs8015773	0.94[ASN][1000 genomes]
rs917066	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs987579	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer 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
3	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv565043	chr14:71395604-71625112	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17093729	CSF3	trans	brain	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71497000-71554200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:71538800-71584800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:71544200-71553200	Weak transcription	Pancreas	Pancrea
4	chr14:71544400-71554800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:71544400-71555600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:71544400-71568800	Weak transcription	Gastric	stomach
7	chr14:71544600-71553400	Weak transcription	Aorta	Aorta
8	chr14:71544800-71553200	Weak transcription	Right Ventricle	heart
9	chr14:71544800-71554600	Weak transcription	HepG2	liver
10	chr14:71544800-71561400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr14:71544800-71571800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr14:71544800-71572000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr14:71544800-71575400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr14:71544800-71581400	Weak transcription	Small Intestine	intestine
15	chr14:71545200-71555000	Weak transcription	Placenta	Placenta
16	chr14:71545200-71555000	Weak transcription	HUVEC	blood vessel
17	chr14:71545200-71556000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr14:71545200-71556400	Weak transcription	Fetal Heart	heart
19	chr14:71545400-71552400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr14:71545400-71554800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr14:71545400-71555600	Weak transcription	NH-A	brain
22	chr14:71545400-71556000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr14:71545400-71556200	Weak transcription	HSMMtube	muscle
24	chr14:71545400-71556400	Weak transcription	HMEC	breast
25	chr14:71545400-71557600	Weak transcription	Brain Angular Gyrus	brain
26	chr14:71545400-71559400	Weak transcription	NHEK	skin
27	chr14:71545400-71570000	Weak transcription	Psoas Muscle	Psoas
28	chr14:71545400-71572000	Weak transcription	Hela-S3	cervix
29	chr14:71545400-71574800	Weak transcription	NHLF	lung
30	chr14:71545600-71554800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr14:71545600-71555000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr14:71545600-71555000	Weak transcription	A549	lung
33	chr14:71545600-71555600	Weak transcription	Colon Smooth Muscle	Colon
34	chr14:71545800-71552400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr14:71545800-71555000	Weak transcription	Brain Anterior Caudate	brain
36	chr14:71545800-71555600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr14:71545800-71556000	Weak transcription	Brain Substantia Nigra	brain
38	chr14:71545800-71558400	Weak transcription	Colonic Mucosa	Colon
39	chr14:71545800-71558800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr14:71545800-71563600	Weak transcription	Fetal Brain Male	brain
41	chr14:71546000-71555000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr14:71546200-71553200	Weak transcription	Fetal Muscle Leg	muscle
43	chr14:71546200-71555000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr14:71546200-71555000	Weak transcription	Fetal Lung	lung
45	chr14:71546200-71555000	Weak transcription	GM12878-XiMat	blood
46	chr14:71546200-71555600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr14:71546200-71555800	Weak transcription	Fetal Kidney	kidney
48	chr14:71546400-71552800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr14:71546400-71554800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr14:71546400-71555000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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