Variant report

Variant	rs16834746
Chromosome Location	chr1:152879096-152879097
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	TEAD4	chr1:152878279-152879319	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:152878027-152879325	SK-N-SH	brain:	n/a	n/a
3	SIN3AK20	chr1:152878682-152879153	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr1:152878691-152879167	T-47D	breast:	n/a	n/a
5	REST	chr1:152878742-152879133	SK-N-SH	brain:	n/a	n/a
6	MAX	chr1:152878113-152879166	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr1:152878029-152879372	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr1:152878118-152879269	SK-N-SH	brain:	n/a	n/a
9	JUND	chr1:152878270-152879343	SK-N-SH	brain:	n/a	chr1:152878898-152878910 chr1:152878900-152878908
10	GATA3	chr1:152878586-152879288	MCF-7	breast:	n/a	n/a
11	PBX3	chr1:152878145-152879353	SK-N-SH	brain:	n/a	n/a
12	EP300	chr1:152878713-152879132	SK-N-SH_RA	brain:	n/a	chr1:152878793-152878806
13	FOSL2	chr1:152878287-152879266	SK-N-SH	brain:	n/a	chr1:152878898-152878910 chr1:152878900-152878908
14	NR2F2	chr1:152878649-152879245	MCF-7	breast:	n/a	n/a
15	RXRA	chr1:152878331-152879269	SK-N-SH	brain:	n/a	chr1:152878907-152878914 chr1:152879200-152879216 chr1:152878818-152878832
16	TEAD4	chr1:152878276-152879357	SK-N-SH	brain:	n/a	n/a
17	BHLHE40	chr1:152878947-152879140	K562	blood:	n/a	n/a
18	TAF1	chr1:152878666-152879153	SK-N-SH	brain:	n/a	n/a
19	JUND	chr1:152878243-152879327	SK-N-SH	brain:	n/a	chr1:152878898-152878910 chr1:152878900-152878908
20	POLR2A	chr1:152878387-152879112	U87	brain:	n/a	n/a
21	USF1	chr1:152878416-152879211	SK-N-SH	brain:	n/a	n/a
22	NFIC	chr1:152878106-152879332	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr1:152878387-152879146	U87	brain:	n/a	n/a
24	MAX	chr1:152878382-152879266	SK-N-SH	brain:	n/a	n/a
25	EP300	chr1:152878784-152879110	SK-N-SH_RA	brain:	n/a	chr1:152878793-152878806
26	GATA3	chr1:152878033-152879376	SK-N-SH	brain:	n/a	n/a
27	TCF12	chr1:152878148-152879304	SK-N-SH	brain:	n/a	n/a
28	FOSL2	chr1:152878620-152879225	MCF-7	breast:	n/a	chr1:152878898-152878910 chr1:152878900-152878908
29	FOSL2	chr1:152878259-152879323	SK-N-SH	brain:	n/a	chr1:152878898-152878910 chr1:152878900-152878908
30	POLR2A	chr1:152878332-152879210	SK-N-SH	brain:	n/a	n/a
31	EP300	chr1:152878174-152879428	SK-N-SH	brain:	n/a	chr1:152878793-152878806 chr1:152878559-152878566
32	PBX3	chr1:152878355-152879290	SK-N-SH	brain:	n/a	n/a
33	RXRA	chr1:152878282-152879369	SK-N-SH	brain:	n/a	chr1:152878907-152878914 chr1:152879200-152879216 chr1:152878818-152878832
34	GATA3	chr1:152878612-152879319	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152878399..152880574-chr1:152925638..152928874,3	MCF-7	breast:

Variant related genes	Relation type
IVL	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10494280	1.00[EUR][1000 genomes]
rs10494288	1.00[EUR][1000 genomes]
rs10888521	1.00[EUR][1000 genomes]
rs11205126	1.00[EUR][1000 genomes]
rs11205129	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11205130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11205132	0.80[ASN][1000 genomes]
rs11205147	1.00[EUR][1000 genomes]
rs11801996	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11806470	1.00[EUR][1000 genomes]
rs12021601	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes]
rs12022349	0.95[JPT][hapmap]
rs12022870	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes]
rs12023643	1.00[EUR][1000 genomes]
rs12024694	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12028228	0.96[ASN][1000 genomes]
rs12029192	1.00[EUR][1000 genomes]
rs12032522	1.00[EUR][1000 genomes]
rs12034091	1.00[CEU][hapmap]
rs12036697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037754	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12047099	1.00[EUR][1000 genomes]
rs12047225	1.00[EUR][1000 genomes]
rs12047630	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12047888	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12048655	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12239808	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12239812	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12239814	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12406539	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1415973	1.00[EUR][1000 genomes]
rs16834734	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs16834751	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs16834838	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16834871	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1846857	1.00[EUR][1000 genomes]
rs1854779	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1974141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995307	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2229496	0.82[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2339383	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes]
rs2339501	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs28647391	1.00[EUR][1000 genomes]
rs2879484	0.89[ASN][1000 genomes]
rs2879485	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs36090881	1.00[EUR][1000 genomes]
rs3737862	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3820136	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3856020	1.00[EUR][1000 genomes]
rs4041337	1.00[EUR][1000 genomes]
rs4240863	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4240864	1.00[EUR][1000 genomes]
rs4363387	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4523473	0.80[ASN][1000 genomes]
rs4845325	1.00[CEU][hapmap]
rs4845327	0.80[ASN][1000 genomes]
rs4845328	1.00[EUR][1000 genomes]
rs4845494	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4845498	1.00[EUR][1000 genomes]
rs58021079	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58290373	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59837747	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60500053	1.00[EUR][1000 genomes]
rs60566199	0.80[ASN][1000 genomes]
rs61482767	1.00[EUR][1000 genomes]
rs61491150	1.00[EUR][1000 genomes]
rs6668295	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73006590	0.80[ASN][1000 genomes]
rs7517189	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7528862	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs7539232	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7545520	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs7552416	1.00[CEU][hapmap]
rs7553755	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7556490	0.81[ASN][1000 genomes]
rs913996	0.86[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv998873	chr1:152869127-152975258	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152876400-152882600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:152876600-152880800	Enhancers	GM12878-XiMat	blood
3	chr1:152876600-152881800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr1:152877200-152879600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:152877400-152879600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:152877600-152879200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:152877600-152879600	Enhancers	NHLF	lung
8	chr1:152877800-152879200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:152878200-152879200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:152878200-152879200	Enhancers	Esophagus	oesophagus
11	chr1:152878200-152879200	Flanking Active TSS	NHDF-Ad	bronchial
12	chr1:152878200-152879200	Flanking Active TSS	NHEK	skin
13	chr1:152878200-152879400	Enhancers	HSMM	muscle
14	chr1:152878400-152879200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:152878600-152879200	Enhancers	Pancreas	Pancrea
16	chr1:152878600-152879400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:152879000-152879200	Flanking Active TSS	HMEC	breast
18	chr1:152879000-152879200	Flanking Active TSS	Osteobl	bone
19	chr1:152879000-152881000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links