Variant report

Variant	rs559231
Chromosome Location	chr18:39644247-39644248
allele	G/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	PBX3	chr18:39643931-39644548	SK-N-SH	brain:	n/a	n/a
2	GATA2	chr18:39643710-39644510	HUVEC	blood vessel:	n/a	chr18:39644321-39644335 chr18:39644326-39644335
3	POLR2A	chr18:39644119-39644406	SK-N-SH	brain:	n/a	n/a
4	FOS	chr18:39644128-39644388	MCF10A-Er-Src	breast:	n/a	chr18:39644248-39644259
5	EP300	chr18:39644035-39644378	SK-N-SH_RA	brain:	n/a	chr18:39644266-39644280 chr18:39644293-39644300
6	GATA3	chr18:39643921-39644694	SK-N-SH	brain:	n/a	chr18:39644326-39644335
7	EP300	chr18:39644156-39644325	SK-N-SH_RA	brain:	n/a	chr18:39644266-39644280 chr18:39644293-39644300
8	PBX3	chr18:39644039-39644423	SK-N-SH	brain:	n/a	n/a
9	FOS	chr18:39644125-39644352	MCF10A-Er-Src	breast:	n/a	chr18:39644248-39644259
10	FOSL2	chr18:39644053-39644476	SK-N-SH	brain:	n/a	n/a
11	JUND	chr18:39644101-39644534	SK-N-SH	brain:	n/a	n/a
12	RXRA	chr18:39643971-39644556	SK-N-SH	brain:	n/a	chr18:39644039-39644048
13	FOS	chr18:39644010-39644520	HUVEC	blood vessel:	n/a	chr18:39644248-39644259
14	FOS	chr18:39644113-39644424	MCF10A-Er-Src	breast:	n/a	chr18:39644248-39644259
15	GATA3	chr18:39643949-39644644	SK-N-SH	brain:	n/a	chr18:39644326-39644335
16	TCF12	chr18:39643985-39644573	SK-N-SH	brain:	n/a	n/a
17	NFIC	chr18:39644015-39644496	SK-N-SH	brain:	n/a	chr18:39644075-39644103

Variant related genes	Relation type
PIK3C3	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1787173	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1788988	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1944967	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4447506	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs477256	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs484350	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs500086	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs503472	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs511605	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs514227	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs515626	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs517864	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs519465	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs523425	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs524793	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs525399	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs52911	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs530113	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs531258	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs533028	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs535626	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs555734	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs573835	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs577955	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582268	0.82[AMR][1000 genomes]
rs584380	0.81[ASN][1000 genomes]
rs587686	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs590912	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs593248	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs600658	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609301	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs620052	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs620344	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622612	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs622939	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs625896	0.90[ASN][1000 genomes]
rs627636	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs629481	0.89[ASN][1000 genomes]
rs638763	0.92[ASN][1000 genomes]
rs639656	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs647512	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs649610	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs664338	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs681048	0.81[ASN][1000 genomes]
rs693020	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
6	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
7	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
8	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
9	nsv1057988	chr18:39618253-39713904	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv1065792	chr18:39619676-39711798	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv1057790	chr18:39621947-39705550	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	esv2762006	chr18:39621947-39713916	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv1063952	chr18:39621947-39718600	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv1064973	chr18:39623604-39711798	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	nsv833631	chr18:39633503-39824091	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr18:39572000-39654400	Weak transcription	Colonic Mucosa	Colon
3	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
4	chr18:39581000-39647400	Weak transcription	Spleen	Spleen
5	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:39585000-39646000	Weak transcription	Pancreas	Pancrea
7	chr18:39585000-39658600	Weak transcription	Small Intestine	intestine
8	chr18:39586600-39647400	Weak transcription	Thymus	Thymus
9	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
10	chr18:39599000-39646000	Weak transcription	Psoas Muscle	Psoas
11	chr18:39601600-39668200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr18:39612200-39647400	Weak transcription	Aorta	Aorta
13	chr18:39612200-39666400	Weak transcription	Gastric	stomach
14	chr18:39612200-39669800	Weak transcription	Fetal Stomach	stomach
15	chr18:39612200-39670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr18:39615000-39649600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr18:39615400-39663400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr18:39618000-39647400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr18:39619200-39656400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr18:39619400-39647600	Weak transcription	Brain Germinal Matrix	brain
21	chr18:39619600-39645600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr18:39619600-39647400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr18:39619800-39662200	Weak transcription	Right Ventricle	heart
24	chr18:39620200-39645800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr18:39620800-39664200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr18:39621200-39646200	Weak transcription	Lung	lung
27	chr18:39621200-39657200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr18:39621600-39644800	Weak transcription	Ovary	ovary
29	chr18:39621800-39644800	Weak transcription	Placenta	Placenta
30	chr18:39622200-39649400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr18:39628600-39666200	Weak transcription	A549	lung
32	chr18:39629000-39649600	Weak transcription	NHLF	lung
33	chr18:39630000-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr18:39630600-39647400	Weak transcription	Colon Smooth Muscle	Colon
35	chr18:39630600-39658600	Weak transcription	Hela-S3	cervix
36	chr18:39630800-39646200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr18:39630800-39650200	Weak transcription	Fetal Kidney	kidney
38	chr18:39631000-39647400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:39631200-39644800	Weak transcription	Fetal Brain Female	brain
40	chr18:39631200-39644800	Weak transcription	Fetal Lung	lung
41	chr18:39631200-39646000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr18:39631200-39646200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr18:39631200-39647000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr18:39631200-39647200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr18:39631200-39647200	Weak transcription	HepG2	liver
46	chr18:39631200-39647400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr18:39631200-39647400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr18:39631200-39650200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr18:39631200-39659800	Weak transcription	Fetal Brain Male	brain
50	chr18:39631400-39646000	Weak transcription	Left Ventricle	heart

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