Variant report

Variant	rs13200858
Chromosome Location	chr6:49636129-49636130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:49633767..49636343-chr6:49654071..49655661,2	K562	blood:
2	chr6:49633093..49639293-chr6:49639855..49647033,9	MCF-7	breast:
3	chr6:49635303..49638158-chr6:49814206..49816242,2	MCF-7	breast:
4	chr6:49499685..49500336-chr6:49635358..49636307,2	MCF-7	breast:
5	chr6:49591740..49593953-chr6:49634897..49637400,2	K562	blood:
6	chr6:49635755..49638329-chr6:49659253..49662142,2	MCF-7	breast:
7	chr6:49601828..49604447-chr6:49633369..49636416,3	K562	blood:
8	chr6:49626742..49629910-chr6:49632110..49636465,6	K562	blood:
9	chr6:49517867..49521348-chr6:49634630..49637748,3	MCF-7	breast:
10	chr6:49591732..49594241-chr6:49632240..49636978,5	MCF-7	breast:
11	chr6:49630171..49632452-chr6:49633861..49636514,2	MCF-7	breast:
12	chr6:49600996..49604201-chr6:49633369..49637658,4	K562	blood:
13	chr6:49589869..49592534-chr6:49635879..49637553,2	MCF-7	breast:
14	chr6:49616976..49619169-chr6:49634760..49637899,5	K562	blood:
15	chr6:49516788..49522068-chr6:49633938..49638066,6	MCF-7	breast:
16	chr6:49509048..49512209-chr6:49635643..49638381,3	MCF-7	breast:
17	chr6:49635591..49637764-chr6:49644790..49647207,2	MCF-7	breast:
18	chr6:49499033..49501525-chr6:49634761..49637688,2	MCF-7	breast:
19	chr6:49508712..49510868-chr6:49634841..49637779,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197261	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10485288	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs10485290	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10948520	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948521	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948522	0.90[EUR][1000 genomes]
rs10948526	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs11751801	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs11752114	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11752255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755355	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758714	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs11759060	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11759109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759134	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs11759936	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524346	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12525576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526063	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs12526795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527987	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528045	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs12528363	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528624	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530191	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190702	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs13192504	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13193202	0.87[EUR][1000 genomes]
rs13193306	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs13193315	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13193433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194498	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13194730	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs13194782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196440	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs13196478	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196728	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13197915	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13197952	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs13197954	0.81[EUR][1000 genomes]
rs13198297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198920	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13200205	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13203838	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13205275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206837	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209352	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs13209765	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210122	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs13211415	0.89[EUR][1000 genomes]
rs13212279	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13213036	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213771	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214316	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214494	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215868	0.86[CEU][hapmap]
rs1321615	0.82[ASN][1000 genomes]
rs13217101	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13219640	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1407112	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538194	0.83[CEU][hapmap]
rs17572279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050867	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs2059940	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs2059941	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs2180724	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396914	0.90[EUR][1000 genomes]
rs2518100	1.00[JPT][hapmap]
rs34029456	0.82[EUR][1000 genomes]
rs35255465	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35495000	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35970561	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4613822	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715140	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56384016	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72873865	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs751744	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs996678	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49634000-49637800	Enhancers	K562	blood
2	chr6:49634400-49636200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr6:49634400-49636400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:49634600-49636200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:49634600-49636400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:49634600-49636400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:49634600-49636600	Enhancers	Hela-S3	cervix
8	chr6:49634600-49637000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:49634600-49637200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:49634800-49636200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:49634800-49636600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr6:49635400-49636400	Enhancers	Primary hematopoietic stem cells	blood
13	chr6:49635400-49636400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:49635600-49636200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:49635800-49636400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:49635800-49637600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:49636000-49636400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:49636000-49637600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links