Variant report

Variant	rs659950
Chromosome Location	chr18:39605836-39605837
allele	A/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	ATF2	chr18:39605599-39606500	GM12878	blood:	n/a	n/a
2	RUNX3	chr18:39605785-39606559	GM12878	blood:	n/a	n/a
3	PAX5	chr18:39605823-39606457	GM12878	blood:	n/a	chr18:39605993-39606002
4	NFIC	chr18:39605407-39606621	GM12878	blood:	n/a	n/a
5	IRF4	chr18:39605736-39606377	GM12878	blood:	n/a	n/a
6	MTA3	chr18:39605687-39606489	GM12878	blood:	n/a	n/a
7	NFIC	chr18:39605663-39606622	GM12878	blood:	n/a	n/a
8	BCLAF1	chr18:39605763-39606478	GM12878	blood:	n/a	n/a
9	CUX1	chr18:39605708-39606394	GM12878	blood:	n/a	n/a
10	RELA	chr18:39605802-39606467	GM12878	blood:	n/a	n/a
11	NFATC1	chr18:39605740-39606445	GM12878	blood:	n/a	n/a
12	PML	chr18:39605788-39606512	GM12878	blood:	n/a	n/a
13	STAT5A	chr18:39605826-39606381	GM12878	blood:	n/a	n/a
14	RELA	chr18:39605816-39606587	GM19099	blood:	n/a	n/a
15	MTA3	chr18:39605789-39606394	GM12878	blood:	n/a	n/a
16	MXI1	chr18:39605823-39606372	GM12878	blood:	n/a	n/a
17	FOXM1	chr18:39605755-39606482	GM12878	blood:	n/a	n/a
18	EP300	chr18:39605454-39606459	GM12878	blood:	n/a	n/a
19	FOXM1	chr18:39605771-39606454	GM12878	blood:	n/a	n/a
20	IKZF1	chr18:39605561-39606307	GM12878	blood:	n/a	chr18:39605960-39605968 chr18:39606009-39606017
21	MEF2A	chr18:39605575-39606433	GM12878	blood:	n/a	n/a
22	CEBPB	chr18:39605822-39606494	GM12878	blood:	n/a	n/a
23	ATF2	chr18:39605765-39606562	GM12878	blood:	n/a	n/a
24	IRF4	chr18:39605790-39606393	GM12878	blood:	n/a	n/a
25	EP300	chr18:39605578-39606429	GM12878	blood:	n/a	n/a
26	TBL1XR1	chr18:39605742-39606444	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PIK3C3	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10502776	1.00[CEU][hapmap]
rs1142044	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11873469	1.00[EUR][1000 genomes]
rs11873602	1.00[EUR][1000 genomes]
rs11874766	1.00[EUR][1000 genomes]
rs11874775	1.00[EUR][1000 genomes]
rs11874814	1.00[EUR][1000 genomes]
rs11874830	1.00[EUR][1000 genomes]
rs11876547	1.00[EUR][1000 genomes]
rs11876578	1.00[EUR][1000 genomes]
rs11877901	1.00[EUR][1000 genomes]
rs1540057	1.00[EUR][1000 genomes]
rs16975441	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16975447	1.00[EUR][1000 genomes]
rs16975463	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975466	1.00[EUR][1000 genomes]
rs16975521	1.00[EUR][1000 genomes]
rs2469471	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs490578	1.00[EUR][1000 genomes]
rs493100	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs525369	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs542870	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55655849	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs563840	1.00[EUR][1000 genomes]
rs56411890	1.00[EUR][1000 genomes]
rs56751463	1.00[EUR][1000 genomes]
rs56979511	1.00[EUR][1000 genomes]
rs57208863	1.00[EUR][1000 genomes]
rs575366	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58298297	1.00[EUR][1000 genomes]
rs583163	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58390786	1.00[EUR][1000 genomes]
rs584022	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs586797	1.00[EUR][1000 genomes]
rs58881642	1.00[EUR][1000 genomes]
rs591870	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs593689	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59910026	1.00[AMR][1000 genomes]
rs606366	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs608428	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs616575	1.00[EUR][1000 genomes]
rs633541	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs635560	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs640064	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs640460	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs643772	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs645148	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs647084	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6507453	1.00[EUR][1000 genomes]
rs6507454	1.00[EUR][1000 genomes]
rs655693	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6650669	1.00[EUR][1000 genomes]
rs667346	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs669235	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs670429	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs674380	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs684091	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7229485	1.00[EUR][1000 genomes]
rs7237185	1.00[EUR][1000 genomes]
rs7237815	1.00[EUR][1000 genomes]
rs7238919	1.00[EUR][1000 genomes]
rs7239880	1.00[EUR][1000 genomes]
rs7240066	1.00[EUR][1000 genomes]
rs7241399	1.00[EUR][1000 genomes]
rs7242077	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245131	1.00[EUR][1000 genomes]
rs7343027	1.00[EUR][1000 genomes]
rs73448558	1.00[EUR][1000 genomes]
rs73451096	1.00[EUR][1000 genomes]
rs73452235	1.00[EUR][1000 genomes]
rs73452297	1.00[EUR][1000 genomes]
rs73452300	1.00[EUR][1000 genomes]
rs73453013	1.00[EUR][1000 genomes]
rs73454552	1.00[EUR][1000 genomes]
rs73454573	1.00[EUR][1000 genomes]
rs73454580	1.00[EUR][1000 genomes]
rs73454581	1.00[EUR][1000 genomes]
rs73454593	1.00[EUR][1000 genomes]
rs73454596	1.00[EUR][1000 genomes]
rs73454602	1.00[EUR][1000 genomes]
rs73950814	1.00[EUR][1000 genomes]
rs8084037	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8085708	1.00[EUR][1000 genomes]
rs8089142	1.00[EUR][1000 genomes]
rs8090403	1.00[EUR][1000 genomes]
rs8095945	1.00[EUR][1000 genomes]
rs9948650	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9965647	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1066029	chr18:39322920-39623625	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv543686	chr18:39322920-39623625	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv909567	chr18:39470190-39652939	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39536000-39621800	Weak transcription	Stomach Mucosa	stomach
2	chr18:39536800-39633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr18:39564600-39606400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr18:39572000-39654400	Weak transcription	Colonic Mucosa	Colon
6	chr18:39577400-39610000	Weak transcription	Fetal Brain Male	brain
7	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
8	chr18:39581000-39609200	Weak transcription	Fetal Intestine Small	intestine
9	chr18:39581000-39610200	Weak transcription	Aorta	Aorta
10	chr18:39581000-39647400	Weak transcription	Spleen	Spleen
11	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr18:39584600-39618600	Weak transcription	NHLF	lung
13	chr18:39585000-39611400	Weak transcription	Gastric	stomach
14	chr18:39585000-39646000	Weak transcription	Pancreas	Pancrea
15	chr18:39585000-39658600	Weak transcription	Small Intestine	intestine
16	chr18:39585200-39610400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr18:39585200-39612000	Weak transcription	NHEK	skin
18	chr18:39585400-39627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr18:39585600-39610200	Weak transcription	Brain Angular Gyrus	brain
20	chr18:39585600-39622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr18:39586000-39610200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr18:39586400-39613000	Weak transcription	Brain Substantia Nigra	brain
23	chr18:39586400-39619000	Weak transcription	HUVEC	blood vessel
24	chr18:39586600-39610400	Weak transcription	Right Ventricle	heart
25	chr18:39586600-39647400	Weak transcription	Thymus	Thymus
26	chr18:39587000-39619400	Weak transcription	Lung	lung
27	chr18:39587200-39610600	Weak transcription	Fetal Stomach	stomach
28	chr18:39587200-39611400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr18:39587200-39614200	Weak transcription	Ovary	ovary
30	chr18:39589800-39606400	Strong transcription	HSMM	muscle
31	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
32	chr18:39590800-39607800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr18:39591800-39609800	Weak transcription	Brain Anterior Caudate	brain
34	chr18:39591800-39610800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr18:39592200-39629400	Weak transcription	Fetal Brain Female	brain
36	chr18:39594000-39609200	Weak transcription	Hela-S3	cervix
37	chr18:39594000-39614400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr18:39594600-39638800	Weak transcription	K562	blood
39	chr18:39595400-39608400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr18:39596000-39609800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr18:39596200-39618800	Weak transcription	Brain Germinal Matrix	brain
42	chr18:39597000-39610400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr18:39597200-39609800	Weak transcription	HMEC	breast
44	chr18:39597400-39622400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr18:39599000-39646000	Weak transcription	Psoas Muscle	Psoas
46	chr18:39599400-39607000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr18:39600400-39609800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr18:39601400-39609800	Weak transcription	NHDF-Ad	bronchial
49	chr18:39601600-39609200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr18:39601600-39609400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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