Variant report

Variant	rs1361565
Chromosome Location	chr1:158985135-158985136
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	MYC	chr1:158984303-158985747	MCF10A-Er-Src	breast:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
2	STAT3	chr1:158984797-158985579	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:158985126-158986008	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:158985081-158986037	GM12892	blood:	n/a	n/a
5	MXI1	chr1:158984946-158985878	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:158985073-158985810	GM12878	blood:	n/a	n/a
7	CUX1	chr1:158985077-158985708	GM12878	blood:	n/a	chr1:158985138-158985152
8	MYC	chr1:158985032-158985656	K562	blood:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
9	MAX	chr1:158985115-158985744	GM12878	blood:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
10	SPI1	chr1:158985017-158986042	GM12878	blood:	n/a	chr1:158985815-158985822
11	MTA3	chr1:158985113-158985899	GM12878	blood:	n/a	n/a
12	MYC	chr1:158985122-158985773	NB4	blood:	n/a	chr1:158985408-158985418 chr1:158985381-158985391
13	POLR2A	chr1:158985023-158986067	U87	brain:	n/a	n/a
14	FOS	chr1:158984686-158985642	MCF10A-Er-Src	breast:	n/a	chr1:158984843-158984851 chr1:158985454-158985465 chr1:158985454-158985461
15	POLR2A	chr1:158983414-158985843	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:158981852-158987235	MCF10A-Er-Src	breast:	n/a	n/a
17	ATF2	chr1:158985129-158985827	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:158978464-158986840	GM12892	blood:	n/a	n/a
19	TEAD4	chr1:158985128-158985606	K562	blood:	n/a	n/a
20	PML	chr1:158985111-158985858	GM12878	blood:	n/a	n/a
21	MYC	chr1:158984174-158985679	MCF10A-Er-Src	breast:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
22	MAX	chr1:158985057-158985729	SK-N-SH	brain:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
23	POLR2A	chr1:158985096-158985805	HL-60	blood:	n/a	n/a
24	MAX	chr1:158985105-158985721	SK-N-SH	brain:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
25	E2F6	chr1:158985084-158985649	H1-hESC	embryonic stem cell:	n/a	chr1:158985207-158985216
26	TCF12	chr1:158985056-158985815	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr1:158981523-158987265	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:158984628-158985937	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr1:158985084-158985923	GM12892	blood:	n/a	n/a
30	POLR2A	chr1:158978384-158985943	GM19193	blood:	n/a	n/a
31	MAX	chr1:158985098-158985744	NB4	blood:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
32	BHLHE40	chr1:158985101-158985707	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:158984975-158985884	U87	brain:	n/a	n/a
34	RUNX3	chr1:158985065-158985696	GM12878	blood:	n/a	n/a
35	JUN	chr1:158985135-158985597	K562	blood:	n/a	chr1:158985454-158985461
36	FOS	chr1:158984785-158985718	HUVEC	blood vessel:	n/a	chr1:158984843-158984851 chr1:158985454-158985465 chr1:158985454-158985461
37	ELF1	chr1:158985112-158985752	SK-N-SH	brain:	n/a	chr1:158985398-158985411
38	MXI1	chr1:158985040-158985924	IMR90	lung:	n/a	n/a
39	POLR2A	chr1:158981580-158990399	GM12891	blood:	n/a	n/a
40	MAX	chr1:158985091-158985661	HCT-116	colon:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
41	POLR2A	chr1:158985101-158986119	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr1:158981297-158987303	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:158985023-158985948	U87	brain:	n/a	n/a
44	POLR2A	chr1:158978350-158987224	GM18505	blood:	n/a	n/a
45	BCLAF1	chr1:158985083-158985898	GM12878	blood:	n/a	n/a
46	ATF2	chr1:158985128-158985741	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:158978475-158987184	GM19099	blood:	n/a	n/a
48	NFIC	chr1:158985123-158985750	GM12878	blood:	n/a	n/a
49	MAX	chr1:158985131-158985661	Hela-S3	cervix:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
50	SETDB1	chr1:158984848-158985570	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11539423	0.88[AMR][1000 genomes]
rs12727764	0.92[MEX][hapmap]
rs12728586	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12734915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12738378	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12739704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12755219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361564	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16841500	0.88[AMR][1000 genomes]
rs1956	0.88[AMR][1000 genomes]
rs4262539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66519738	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72704976	0.88[AMR][1000 genomes]
rs7526724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs856047	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158976000-159000800	Weak transcription	Gastric	stomach
2	chr1:158977200-158990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:158978800-158985800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:158981200-158985400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:158981200-158985400	Weak transcription	Pancreas	Pancrea
7	chr1:158981200-158986400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:158981600-158986000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr1:158982000-158988000	Weak transcription	Fetal Brain Male	brain
10	chr1:158982600-158985400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:158982600-158985400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:158982600-158985400	Weak transcription	Fetal Stomach	stomach
13	chr1:158982600-158986200	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
15	chr1:158982800-158985200	Weak transcription	Stomach Mucosa	stomach
16	chr1:158982800-158985400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:158982800-158985400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:158982800-158985400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:158982800-158985400	Weak transcription	NH-A	brain
20	chr1:158982800-158987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:158982800-158989600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:158982800-159000200	Weak transcription	Aorta	Aorta
23	chr1:158983000-158986000	Genic enhancers	Osteobl	bone
24	chr1:158983000-158987200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:158983200-158985400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:158983200-158985400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:158983200-158985400	Weak transcription	Lung	lung
28	chr1:158983200-158986000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:158983400-158985200	Genic enhancers	Primary hematopoietic stem cells	blood
30	chr1:158983400-158985400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr1:158983400-158985600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:158983400-158985800	Enhancers	Small Intestine	intestine
33	chr1:158983400-158987200	Transcr. at gene 5' and 3'	Dnd41	blood
34	chr1:158983600-158985400	Weak transcription	Colonic Mucosa	Colon
35	chr1:158983600-158985600	Weak transcription	Placenta	Placenta
36	chr1:158983600-158987200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
37	chr1:158983600-158988000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:158983800-158985400	Genic enhancers	HUVEC	blood vessel
39	chr1:158983800-158986000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:158983800-158986000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:158984000-158985200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
42	chr1:158984000-158985200	Genic enhancers	Primary T cells from cord blood	blood
43	chr1:158984000-158985400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr1:158984000-158985400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:158984000-158986000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
46	chr1:158984000-158986200	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:158984000-158986400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:158984000-158986600	Genic enhancers	HSMMtube	muscle
49	chr1:158984000-158988000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:158984000-158991600	Strong transcription	Fetal Lung	lung

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