Variant report

Variant	rs1361564
Chromosome Location	chr1:158985316-158985317
allele	C/G
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	POLR2A	chr1:158985137-158985926	GM12892	blood:	n/a	n/a
2	MYC	chr1:158984303-158985747	MCF10A-Er-Src	breast:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
3	FOS	chr1:158985268-158985641	MCF10A-Er-Src	breast:	n/a	chr1:158985454-158985465 chr1:158985454-158985461
4	TAF1	chr1:158985297-158985626	SK-N-SH	brain:	n/a	n/a
5	MXI1	chr1:158985287-158985639	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:158985174-158986033	GM12878	blood:	n/a	n/a
7	STAT3	chr1:158984797-158985579	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:158985126-158986008	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:158985081-158986037	GM12892	blood:	n/a	n/a
10	MAX	chr1:158985207-158985581	H1-hESC	embryonic stem cell:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
11	USF1	chr1:158985206-158985694	SK-N-SH	brain:	n/a	n/a
12	MAX	chr1:158985186-158985611	H1-hESC	embryonic stem cell:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
13	ETS1	chr1:158985217-158985659	GM12878	blood:	n/a	chr1:158985402-158985416 chr1:158985402-158985411 chr1:158985401-158985414
14	CEBPB	chr1:158985259-158985911	IMR90	lung:	n/a	chr1:158985893-158985905
15	MXI1	chr1:158984946-158985878	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:158985181-158985785	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr1:158985199-158985693	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:158985266-158985601	Gliobla	brain:	n/a	n/a
19	POLR2A	chr1:158985202-158985941	HL-60	blood:	n/a	n/a
20	POLR2A	chr1:158985073-158985810	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:158985168-158985932	GM12891	blood:	n/a	n/a
22	ATF1	chr1:158985296-158985598	K562	blood:	n/a	n/a
23	USF1	chr1:158985268-158985603	SK-N-SH_RA	brain:	n/a	n/a
24	MAX	chr1:158985202-158985842	Hela-S3	cervix:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
25	POLR2A	chr1:158985174-158985772	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:158985206-158985856	HUVEC	blood vessel:	n/a	n/a
27	MYC	chr1:158985217-158985600	K562	blood:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
28	POLR2A	chr1:158985274-158985731	GM12878	blood:	n/a	n/a
29	TCF12	chr1:158985285-158985624	GM12878	blood:	n/a	n/a
30	ELF1	chr1:158985259-158985769	GM12878	blood:	n/a	chr1:158985398-158985411
31	MAFK	chr1:158985310-158985594	IMR90	lung:	n/a	chr1:158985441-158985452 chr1:158985441-158985452 chr1:158985440-158985451 chr1:158985440-158985451
32	USF1	chr1:158985312-158985556	K562	blood:	n/a	n/a
33	CUX1	chr1:158985077-158985708	GM12878	blood:	n/a	chr1:158985138-158985152
34	TAF1	chr1:158985260-158985612	Hela-S3	cervix:	n/a	n/a
35	MYC	chr1:158985032-158985656	K562	blood:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
36	USF2	chr1:158985258-158985713	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:158985247-158985666	Hela-S3	cervix:	n/a	n/a
38	E2F6	chr1:158985229-158985616	K562	blood:	n/a	n/a
39	MAX	chr1:158985178-158985643	GM12878	blood:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
40	E2F6	chr1:158985296-158985548	K562	blood:	n/a	n/a
41	MAX	chr1:158985115-158985744	GM12878	blood:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
42	SPI1	chr1:158985017-158986042	GM12878	blood:	n/a	chr1:158985815-158985822
43	E2F6	chr1:158985222-158985553	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr1:158985229-158985828	Hela-S3	cervix:	n/a	n/a
45	SIN3AK20	chr1:158985229-158985636	SK-N-SH	brain:	n/a	n/a
46	CHD1	chr1:158985233-158985895	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:158985283-158985632	GM12878	blood:	n/a	n/a
48	GABPA	chr1:158985211-158985760	SK-N-SH	brain:	n/a	n/a
49	MAX	chr1:158985250-158985543	A549	lung:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
50	USF1	chr1:158985228-158985612	SK-N-SH_RA	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	1.00[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]
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]
rs1361565	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:104 , 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	chr1:158982800-158985400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:158982800-158985400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:158982800-158985400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:158982800-158985400	Weak transcription	NH-A	brain
19	chr1:158982800-158987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:158982800-158989600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:158982800-159000200	Weak transcription	Aorta	Aorta
22	chr1:158983000-158986000	Genic enhancers	Osteobl	bone
23	chr1:158983000-158987200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:158983200-158985400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:158983200-158985400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:158983200-158985400	Weak transcription	Lung	lung
27	chr1:158983200-158986000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:158983400-158985400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:158983400-158985600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:158983400-158985800	Enhancers	Small Intestine	intestine
31	chr1:158983400-158987200	Transcr. at gene 5' and 3'	Dnd41	blood
32	chr1:158983600-158985400	Weak transcription	Colonic Mucosa	Colon
33	chr1:158983600-158985600	Weak transcription	Placenta	Placenta
34	chr1:158983600-158987200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
35	chr1:158983600-158988000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:158983800-158985400	Genic enhancers	HUVEC	blood vessel
37	chr1:158983800-158986000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:158983800-158986000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:158984000-158985400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:158984000-158985400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:158984000-158986000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
42	chr1:158984000-158986200	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:158984000-158986400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:158984000-158986600	Genic enhancers	HSMMtube	muscle
45	chr1:158984000-158988000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:158984000-158991600	Strong transcription	Fetal Lung	lung
47	chr1:158984000-159000800	Weak transcription	Right Ventricle	heart
48	chr1:158984200-158985400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:158984200-158985400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:158984200-158985400	Weak transcription	Ovary	ovary

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