Variant report

Variant	rs3753813
Chromosome Location	chr1:180123538-180123539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:316)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:316 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:180123335-180123869	U87	brain:	n/a	n/a
2	RFX5	chr1:180123515-180123663	HepG2	liver:	n/a	chr1:180123573-180123588
3	POLR2A	chr1:180122889-180123878	SK-N-SH	brain:	n/a	n/a
4	HEY1	chr1:180123299-180124184	HepG2	liver:	n/a	chr1:180123698-180123713
5	POLR2A	chr1:180122966-180123901	HL-60	blood:	n/a	n/a
6	WRNIP1	chr1:180123109-180123852	GM12878	blood:	n/a	n/a
7	TBP	chr1:180123473-180124168	Hela-S3	cervix:	n/a	n/a
8	EP300	chr1:180123489-180123727	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:180123211-180124255	GM18505	blood:	n/a	n/a
10	HMGN3	chr1:180123412-180124578	K562	blood:	n/a	n/a
11	MYC	chr1:180123258-180124332	NB4	blood:	n/a	n/a
12	MXI1	chr1:180123165-180124738	GM12878	blood:	n/a	chr1:180123364-180123379 chr1:180123945-180123954 chr1:180124358-180124367
13	POLR2A	chr1:180123249-180123873	GM12892	blood:	n/a	n/a
14	ELK1	chr1:180123498-180123793	K562	blood:	n/a	n/a
15	JUND	chr1:180123516-180124239	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:180123195-180124269	GM19099	blood:	n/a	n/a
17	POLR2A	chr1:180123371-180124265	HUVEC	blood vessel:	n/a	n/a
18	NR2F2	chr1:180123191-180123857	K562	blood:	n/a	n/a
19	GABPA	chr1:180123327-180124275	K562	blood:	n/a	chr1:180123962-180123971
20	JUND	chr1:180123048-180124218	K562	blood:	n/a	n/a
21	SIX5	chr1:180123395-180123794	A549	lung:	n/a	n/a
22	POLR2A	chr1:180123386-180123874	K562	blood:	n/a	n/a
23	ATF3	chr1:180123202-180123883	A549	lung:	n/a	n/a
24	STAT5A	chr1:180123385-180123919	K562	blood:	n/a	n/a
25	REST	chr1:180123447-180123735	SK-N-SH	brain:	n/a	n/a
26	EP300	chr1:180123527-180123739	K562	blood:	n/a	n/a
27	IRF1	chr1:180123401-180124177	K562	blood:	n/a	n/a
28	POLR2A	chr1:180123325-180124208	U87	brain:	n/a	n/a
29	EGR1	chr1:180123475-180124602	K562	blood:	n/a	chr1:180124313-180124327 chr1:180123851-180123865 chr1:180124373-180124387
30	SIN3A	chr1:180123052-180125035	H1-hESC	embryonic stem cell:	n/a	chr1:180123821-180123834 chr1:180123945-180123954
31	POLR2A	chr1:180123346-180123865	HepG2	liver:	n/a	n/a
32	RUNX3	chr1:180123359-180124324	GM12878	blood:	n/a	n/a
33	MAZ	chr1:180123331-180124266	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr1:180122896-180124310	PBDE	blood:	n/a	n/a
35	MAZ	chr1:180123089-180125392	IMR90	lung:	n/a	n/a
36	MYC	chr1:180123270-180124203	H1-hESC	embryonic stem cell:	n/a	n/a
37	POU2F2	chr1:180123112-180123888	GM12878	blood:	n/a	n/a
38	TBL1XR1	chr1:180123467-180123735	K562	blood:	n/a	n/a
39	POLR2A	chr1:180123135-180124468	PFSK-1	brain:	n/a	n/a
40	SIN3A	chr1:180123341-180123736	GM12878	blood:	n/a	n/a
41	UBTF	chr1:180123366-180124284	K562	blood:	n/a	n/a
42	POLR2A	chr1:180123320-180124214	U87	brain:	n/a	n/a
43	TEAD4	chr1:180123104-180123854	K562	blood:	n/a	n/a
44	TAF1	chr1:180123488-180124301	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr1:180122678-180124264	MCF10A-Er-Src	breast:	n/a	n/a
46	GABPA	chr1:180123440-180123870	K562	blood:	n/a	n/a
47	ELF1	chr1:180123354-180123882	K562	blood:	n/a	n/a
48	ELF1	chr1:180123165-180124095	HCT-116	colon:	n/a	chr1:180123984-180123996
49	POLR2A	chr1:180123427-180123904	A549	lung:	n/a	n/a
50	POLR2A	chr1:180123347-180123885	A549	lung:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180123409..180123996-chr11:62609034..62610004,2	Hela-S3	cervix:
2	chr1:8937559..8938400-chr1:180123331..180124251,2	Hela-S3	cervix:
3	chr1:179844379..179846987-chr1:180122185..180123975,2	MCF-7	breast:
4	chr1:180123151..180123859-chr12:16034873..16035578,2	HCT-116	colon:
5	chr1:179844894..179847778-chr1:180122782..180124340,2	K562	blood:
6	chr1:179849468..179853023-chr1:180122560..180126275,4	K562	blood:
7	chr1:180123484..180124292-chr16:46722902..46723601,2	HCT-116	colon:
8	chr1:180123093..180123878-chr14:81687002..81687977,2	Hela-S3	cervix:
9	chr1:179843719..179847778-chr1:180121939..180127812,8	K562	blood:
10	chr1:180123486..180124377-chrX:53350238..53351237,2	MCF-7	breast:
11	chr1:180122867..180124515-chr12:122237701..122240027,2	MCF-7	breast:
12	chr1:179923898..179926923-chr1:180121889..180124249,4	MCF-7	breast:
13	chr1:180109932..180112525-chr1:180121644..180123894,2	MCF-7	breast:
14	chr1:180123247..180124010-chr10:106097820..106098659,2	Hela-S3	cervix:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACBD6-3	chr1:180123134-180123641	NONHSAT008242

No data

Variant related genes	Relation type
QSOX1	TF binding region
ENSG00000236269	Chromatin interaction
ENSG00000091651	Chromatin interaction
ENSG00000151491	Chromatin interaction
ENSG00000165417	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000069329	Chromatin interaction
ENSG00000169905	Chromatin interaction
ENSG00000023734	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000124313	Chromatin interaction
ENSG00000148841	Chromatin interaction
ENSG00000074800	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12022994	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12034707	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12034708	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036985	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275809	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2298205	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3738115	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3753806	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3753807	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3753808	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3753810	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3767168	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3767186	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3767187	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3767188	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3767194	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767195	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3795506	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3820309	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55700062	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55710113	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56150169	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56151584	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56882898	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57163857	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57306173	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57587074	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57807046	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59644903	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60471708	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60836685	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72710693	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72710699	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1007590	chr1:180121480-180236452	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv999104	chr1:180121480-180242659	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv3355160	chr1:180122754-180125702	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180122400-180124600	Active TSS	Esophagus	oesophagus
2	chr1:180122400-180125000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:180122800-180123600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:180122800-180123600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr1:180122800-180123600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:180122800-180123600	Flanking Active TSS	Hela-S3	cervix
7	chr1:180122800-180123600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr1:180122800-180124400	Active TSS	Fetal Brain Female	brain
9	chr1:180122800-180124800	Active TSS	Colon Smooth Muscle	Colon
10	chr1:180122800-180124800	Active TSS	Fetal Kidney	kidney
11	chr1:180122800-180125000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:180122800-180125200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:180122800-180125400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:180123000-180123600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr1:180123000-180123600	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr1:180123000-180123600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr1:180123000-180123600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr1:180123000-180123600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr1:180123000-180123600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr1:180123000-180123600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr1:180123000-180123600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:180123000-180123600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:180123000-180123600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr1:180123000-180123600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:180123000-180123600	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr1:180123000-180123600	Flanking Active TSS	Fetal Brain Male	brain
27	chr1:180123000-180123600	Flanking Active TSS	Fetal Thymus	thymus
28	chr1:180123000-180123600	Flanking Active TSS	Pancreas	Pancrea
29	chr1:180123000-180123600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr1:180123000-180123600	Flanking Active TSS	HMEC	breast
31	chr1:180123000-180123600	Flanking Active TSS	HUVEC	blood vessel
32	chr1:180123000-180123600	Flanking Active TSS	NHEK	skin
33	chr1:180123000-180123600	Flanking Active TSS	NHLF	lung
34	chr1:180123000-180123800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:180123000-180123800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr1:180123000-180124000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:180123000-180124400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:180123000-180124400	Active TSS	Fetal Muscle Trunk	muscle
39	chr1:180123000-180124600	Active TSS	Psoas Muscle	Psoas
40	chr1:180123000-180124800	Active TSS	Aorta	Aorta
41	chr1:180123000-180125000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:180123000-180125200	Active TSS	H9 Cell Line	embryonic stem cell
43	chr1:180123000-180125600	Active TSS	Left Ventricle	heart
44	chr1:180123200-180123600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:180123200-180123600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:180123200-180123600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:180123200-180123600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr1:180123200-180123600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:180123200-180123600	Flanking Active TSS	Colonic Mucosa	Colon
50	chr1:180123200-180123600	Flanking Active TSS	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links