Variant report

Variant	rs842799
Chromosome Location	chr1:192921361-192921362
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	RUNX3	chr1:192921139-192921457	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:192921163-192921588	SK-N-SH	brain:	n/a	n/a
3	MYC	chr1:192921254-192921498	MCF10A-Er-Src	breast:	n/a	chr1:192921263-192921272
4	POLR2A	chr1:192921289-192921509	SK-N-SH	brain:	n/a	n/a
5	RCOR1	chr1:192920915-192921816	IMR90	lung:	n/a	n/a
6	GATA3	chr1:192921047-192921727	SK-N-SH	brain:	n/a	n/a
7	MAFK	chr1:192921191-192921567	K562	blood:	n/a	n/a
8	JUND	chr1:192921091-192921698	SK-N-SH	brain:	n/a	n/a
9	JUND	chr1:192920934-192921765	SK-N-SH	brain:	n/a	n/a
10	MAX	chr1:192921197-192921579	SK-N-SH	brain:	n/a	chr1:192921263-192921272
11	FOS	chr1:192921068-192921567	MCF10A-Er-Src	breast:	n/a	chr1:192921365-192921376
12	GATA2	chr1:192921161-192921590	HUVEC	blood vessel:	n/a	n/a
13	EP300	chr1:192921164-192921737	SK-N-SH	brain:	n/a	n/a
14	E2F4	chr1:192921117-192921554	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr1:192921028-192921678	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr1:192921197-192921483	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr1:192921121-192921679	U87	brain:	n/a	n/a
18	FOSL2	chr1:192921074-192921734	SK-N-SH	brain:	n/a	n/a
19	FOS	chr1:192921143-192921576	MCF10A-Er-Src	breast:	n/a	chr1:192921365-192921376
20	POU2F2	chr1:192921100-192921475	GM12891	blood:	n/a	chr1:192921257-192921272 chr1:192921260-192921269 chr1:192921258-192921272 chr1:192921255-192921276 chr1:192921261-192921268 chr1:192921262-192921275 chr1:192921259-192921269 chr1:192921262-192921275 chr1:192921261-192921269 chr1:192921262-192921275 chr1:192921260-192921270 chr1:192921258-192921270 chr1:192921256-192921274 chr1:192921260-192921271 chr1:192921259-192921269
21	STAT3	chr1:192921067-192922146	MCF10A-Er-Src	breast:	n/a	chr1:192921799-192921822 chr1:192921800-192921808 chr1:192921814-192921822 chr1:192921811-192921825
22	MYC	chr1:192921124-192921517	MCF10A-Er-Src	breast:	n/a	chr1:192921263-192921272
23	CEBPB	chr1:192921248-192921562	K562	blood:	n/a	n/a
24	ATF2	chr1:192921016-192921515	GM12878	blood:	n/a	n/a
25	FOS	chr1:192921057-192921649	HUVEC	blood vessel:	n/a	chr1:192921365-192921376
26	PBX3	chr1:192921093-192921766	SK-N-SH	brain:	n/a	n/a
27	CEBPB	chr1:192921175-192922081	IMR90	lung:	n/a	n/a
28	RAD21	chr1:192921328-192921515	SK-N-SH_RA	brain:	n/a	n/a
29	EP300	chr1:192921139-192921572	SK-N-SH_RA	brain:	n/a	n/a
30	STAT3	chr1:192921112-192921463	MCF10A-Er-Src	breast:	n/a	n/a
31	JUND	chr1:192921204-192921544	K562	blood:	n/a	n/a
32	FOSL2	chr1:192921122-192921650	SK-N-SH	brain:	n/a	n/a
33	BACH1	chr1:192921331-192921458	K562	blood:	n/a	n/a
34	MAFF	chr1:192921191-192921524	K562	blood:	n/a	n/a
35	POU2F2	chr1:192921036-192921450	GM12878	blood:	n/a	chr1:192921257-192921272 chr1:192921260-192921269 chr1:192921258-192921272 chr1:192921255-192921276 chr1:192921261-192921268 chr1:192921262-192921275 chr1:192921259-192921269 chr1:192921262-192921275 chr1:192921261-192921269 chr1:192921262-192921275 chr1:192921260-192921270 chr1:192921258-192921270 chr1:192921256-192921274 chr1:192921260-192921271 chr1:192921259-192921269
36	NFIC	chr1:192921087-192921720	SK-N-SH	brain:	n/a	n/a
37	GATA3	chr1:192921077-192921729	SK-N-SH	brain:	n/a	n/a
38	TCF12	chr1:192920923-192921687	SK-N-SH	brain:	n/a	n/a
39	RAD21	chr1:192921239-192921560	SK-N-SH_RA	brain:	n/a	n/a
40	EP300	chr1:192921170-192921626	SK-N-SH_RA	brain:	n/a	n/a
41	MAFK	chr1:192920994-192921538	IMR90	lung:	n/a	chr1:192921121-192921132 chr1:192921123-192921140 chr1:192921120-192921131
42	STAT3	chr1:192921113-192922107	MCF10A-Er-Src	breast:	n/a	chr1:192921799-192921822 chr1:192921800-192921808 chr1:192921814-192921822 chr1:192921811-192921825
43	STAT3	chr1:192921114-192922161	MCF10A-Er-Src	breast:	n/a	chr1:192921799-192921822 chr1:192921800-192921808 chr1:192921814-192921822 chr1:192921811-192921825
44	FOS	chr1:192921036-192922132	MCF10A-Er-Src	breast:	n/a	chr1:192921365-192921376
45	JUN	chr1:192921110-192921579	HUVEC	blood vessel:	n/a	n/a
46	SIN3AK20	chr1:192921228-192921473	PFSK-1	brain:	n/a	n/a
47	JUND	chr1:192921097-192921633	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr1:192921303-192921490	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr1:192920959-192921695	HUVEC	blood vessel:	n/a	n/a
50	TCF12	chr1:192920990-192921813	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UCHL5-1	chr1:192921311-192921639	XLOC_001134
2	lnc-TROVE2-3	chr1:192921310-192921639	NONHSAT008550

Variant related genes	Relation type
LINC01032	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1339589	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1339592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1578163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1612628	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1618583	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1769055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769056	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769057	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769059	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769068	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1769070	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1769071	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1770923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2486494	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2486495	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2486498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2487283	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2487289	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59189492	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6661948	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73068182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73068192	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7546076	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7553594	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs842784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842785	0.81[AFR][1000 genomes]
rs842786	0.81[AFR][1000 genomes]
rs842787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842788	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842800	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842801	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842805	0.93[YRI][hapmap]
rs842806	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842808	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842811	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs863600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs866380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs866381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs946556	1.00[AFR][1000 genomes];1.00[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	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv548660	chr1:192609268-192945348	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv999499	chr1:192909529-192998421	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv535252	chr1:192909529-192998421	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192909000-192936600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:192917600-192927800	Weak transcription	Left Ventricle	heart
3	chr1:192920000-192922400	Enhancers	HUVEC	blood vessel
4	chr1:192920400-192922200	Enhancers	Rectal Smooth Muscle	rectum
5	chr1:192920600-192921600	Enhancers	Fetal Kidney	kidney
6	chr1:192920600-192922400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:192920600-192922400	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr1:192920600-192922600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:192920600-192925200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:192920800-192921400	Enhancers	Fetal Stomach	stomach
11	chr1:192920800-192921600	Enhancers	GM12878-XiMat	blood
12	chr1:192920800-192922000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr1:192920800-192922200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:192920800-192922200	Enhancers	HSMMtube	muscle
15	chr1:192920800-192922400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:192920800-192922400	Enhancers	NHDF-Ad	bronchial
17	chr1:192921000-192921400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:192921000-192921400	Flanking Active TSS	Colon Smooth Muscle	Colon
19	chr1:192921000-192921400	Flanking Active TSS	NH-A	brain
20	chr1:192921000-192921600	Enhancers	Primary B cells from cord blood	blood
21	chr1:192921000-192921600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:192921000-192921600	Active TSS	Stomach Smooth Muscle	stomach
23	chr1:192921000-192922200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:192921000-192922200	Enhancers	HSMM	muscle
25	chr1:192921000-192922200	Enhancers	NHEK	skin
26	chr1:192921000-192922200	Enhancers	NHLF	lung
27	chr1:192921000-192922400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:192921000-192922400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:192921000-192922400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:192921000-192922400	Enhancers	Osteobl	bone
31	chr1:192921200-192921600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:192921200-192921600	Enhancers	A549	lung
33	chr1:192921200-192921600	Enhancers	K562	blood
34	chr1:192921200-192923600	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links