Variant report

Variant	rs6429548
Chromosome Location	chr1:45253628-45253629
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	POLR2A	chr1:45253565-45253636	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45248852..45254229-chr1:45263166..45267959,10	MCF-7	breast:
2	chr1:45253589..45255974-chr1:45285344..45287437,3	MCF-7	breast:
3	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
4	chr1:45246681..45259677-chr1:45281336..45290057,25	MCF-7	breast:
5	chr1:45248400..45253844-chr1:45268438..45273783,8	MCF-7	breast:

Variant related genes	Relation type
BEST4	TF binding region
ENSG00000202444	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000188396	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10127448	0.88[EUR][1000 genomes]
rs10465818	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211030	0.96[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes]
rs11211031	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11211037	0.84[CEU][hapmap];0.91[GIH][hapmap]
rs11211046	0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11211047	0.82[ASN][1000 genomes]
rs11573543	0.87[JPT][hapmap]
rs11584031	0.84[CEU][hapmap]
rs11801067	0.93[EUR][1000 genomes]
rs11808189	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11808852	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12059964	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12094007	0.82[ASN][1000 genomes]
rs12094028	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12120470	0.82[ASN][1000 genomes]
rs12136048	0.92[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12136099	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1226572	0.81[JPT][hapmap]
rs12408818	0.82[ASN][1000 genomes]
rs12568071	0.82[ASN][1000 genomes]
rs12568279	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs12732939	0.89[YRI][hapmap]
rs12746270	0.89[YRI][hapmap]
rs16832228	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs263965	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs263966	0.85[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs263975	0.81[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs263990	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs2983715	0.93[CHD][hapmap];0.87[JPT][hapmap]
rs3795720	0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap]
rs3820586	0.89[YRI][hapmap]
rs452989	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs4542248	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4596943	0.80[ASN][1000 genomes]
rs6656337	0.88[EUR][1000 genomes]
rs6658470	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6666987	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6671255	0.89[EUR][1000 genomes]
rs6678729	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6685176	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6688465	0.82[ASN][1000 genomes]
rs6688710	0.82[EUR][1000 genomes]
rs6689911	0.89[YRI][hapmap]
rs6696675	0.82[ASN][1000 genomes]
rs6698951	0.82[ASN][1000 genomes]
rs746320	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7524446	0.91[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7525308	0.88[ASW][hapmap];0.84[CEU][hapmap];0.94[GIH][hapmap]
rs7526786	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7534487	0.89[YRI][hapmap]
rs7536146	0.92[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs7550170	0.96[CEU][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7554177	0.86[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs7555065	0.96[CEU][hapmap];0.86[YRI][hapmap];0.93[EUR][1000 genomes]
rs932691	0.82[ASN][1000 genomes]
rs9988451	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs9988580	0.96[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
8	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv947252	chr1:45242176-45258816	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6429548	SNORD55	cis	parietal	SCAN
rs6429548	C1orf84	cis	parietal	SCAN
rs6429548	EIF2B3	cis	cerebellum	SCAN
rs6429548	C1orf190	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45245000-45258600	Weak transcription	Hela-S3	cervix
2	chr1:45252000-45255400	Weak transcription	K562	blood
3	chr1:45252400-45253800	Weak transcription	NHDF-Ad	bronchial
4	chr1:45252400-45255400	Weak transcription	NHEK	skin
5	chr1:45252400-45255600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:45252400-45255800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:45252400-45256800	Weak transcription	Stomach Mucosa	stomach
8	chr1:45252400-45264200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:45252400-45265200	Weak transcription	Right Atrium	heart
10	chr1:45252400-45265600	Weak transcription	Gastric	stomach
11	chr1:45252600-45254000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:45252600-45254000	Weak transcription	Spleen	Spleen
13	chr1:45252600-45254200	Weak transcription	Fetal Brain Female	brain
14	chr1:45252600-45256600	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:45252600-45256800	Weak transcription	Pancreas	Pancrea
16	chr1:45252600-45256800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:45252600-45257000	Weak transcription	Fetal Intestine Large	intestine
18	chr1:45252600-45257200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:45252600-45258800	Weak transcription	Esophagus	oesophagus
20	chr1:45252600-45258800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:45252600-45259000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:45252600-45262200	Weak transcription	Placenta	Placenta
23	chr1:45252600-45264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:45252800-45254000	Bivalent Enhancer	HepG2	liver
25	chr1:45252800-45255400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:45252800-45255600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:45252800-45255600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:45252800-45255600	Weak transcription	HMEC	breast
29	chr1:45252800-45257000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:45252800-45257200	Weak transcription	Fetal Intestine Small	intestine
31	chr1:45252800-45258800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:45252800-45258800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:45252800-45259000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:45253200-45253800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:45253400-45254200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:45253400-45254400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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