Variant report

Variant	rs12402781
Chromosome Location	chr1:45258967-45258968
allele	G/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45194659..45196445-chr1:45258942..45260527,2	MCF-7	breast:
2	chr1:45257422..45260349-chr1:45347384..45350306,2	K562	blood:
3	chr1:45253913..45255950-chr1:45257305..45259457,2	MCF-7	breast:
4	chr1:45185596..45187362-chr1:45255952..45259330,3	MCF-7	breast:
5	chr1:45258952..45260849-chr1:45465146..45466652,2	MCF-7	breast:
6	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
7	chr1:45246681..45259677-chr1:45281336..45290057,25	MCF-7	breast:
8	chr1:45257179..45260410-chr1:45476355..45479438,4	K562	blood:
9	chr1:45257179..45261874-chr1:45476446..45479576,6	K562	blood:
10	chr1:45258217..45261101-chr1:45283716..45287157,8	MCF-7	breast:
11	chr1:45187577..45189400-chr1:45255993..45258974,2	MCF-7	breast:
12	chr1:45257627..45260973-chr1:45264526..45267678,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202444	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000117425	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10159318	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs1022814	0.81[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap]
rs11211042	0.88[CEU][hapmap]
rs11211052	0.80[CEU][hapmap]
rs11211062	0.81[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs11211063	0.80[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap]
rs12057238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057414	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12072767	0.97[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs12093313	0.81[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs12095412	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12402452	0.81[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs12403201	0.81[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs12404160	0.93[ASN][1000 genomes]
rs12405721	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs12407290	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs12407565	0.81[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap]
rs12407627	0.83[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];0.92[ASN][1000 genomes]
rs16832251	0.88[CEU][hapmap]
rs16832301	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs17390328	0.81[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17391430	0.83[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.92[ASN][1000 genomes]
rs17392632	0.81[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17883304	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17885815	0.93[ASN][1000 genomes]
rs2102035	0.84[JPT][hapmap]
rs2295996	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs263979	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs264002	0.81[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs3795712	0.83[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs3795715	0.87[CEU][hapmap];0.80[CHB][hapmap];0.89[ASN][1000 genomes]
rs3795718	0.88[CEU][hapmap]
rs3806398	0.92[ASN][1000 genomes]
rs3889352	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs3889822	0.81[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs3923304	0.88[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs392410	1.00[JPT][hapmap]
rs4073112	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4082644	0.81[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap]
rs41269079	0.92[ASN][1000 genomes]
rs435311	0.81[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs4520451	0.93[ASN][1000 genomes]
rs4565758	0.87[ASN][1000 genomes]
rs471564	0.81[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs55703843	0.84[ASN][1000 genomes]
rs58603818	0.82[ASN][1000 genomes]
rs59895800	0.89[ASN][1000 genomes]
rs60452778	0.93[ASN][1000 genomes]
rs608649	0.81[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs637224	0.80[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs72674017	0.89[ASN][1000 genomes]
rs72674023	0.92[ASN][1000 genomes]
rs7515226	0.81[CEU][hapmap];0.92[JPT][hapmap]
rs7519592	0.81[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.93[TSI][hapmap]
rs7529213	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap]

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	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12402781	C1orf84	cis	parietal	SCAN
rs12402781	EBNA1BP2	cis	cerebellum	SCAN
rs12402781	MED8	cis	cerebellum	SCAN
rs12402781	ZNF691	cis	parietal	SCAN
rs12402781	CDC20	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45252400-45264200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:45252400-45265200	Weak transcription	Right Atrium	heart
3	chr1:45252400-45265600	Weak transcription	Gastric	stomach
4	chr1:45252600-45259000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:45252600-45262200	Weak transcription	Placenta	Placenta
6	chr1:45252600-45264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:45252800-45259000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:45255400-45259600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:45255400-45259800	Enhancers	K562	blood
10	chr1:45255800-45259000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:45256000-45264200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:45256000-45264800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:45256000-45265200	Weak transcription	NHEK	skin
14	chr1:45256800-45259200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:45257400-45264800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:45257600-45259000	Weak transcription	Fetal Intestine Large	intestine
17	chr1:45258400-45259400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:45258600-45259200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:45258600-45259400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:45258600-45259400	Enhancers	HMEC	breast
21	chr1:45258600-45259600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:45258800-45259000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:45258800-45259000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:45258800-45259000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:45258800-45259200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:45258800-45259200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:45258800-45259400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:45258800-45259400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr1:45258800-45259400	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr1:45258800-45259400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:45258800-45259400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:45258800-45259400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr1:45258800-45259400	Flanking Active TSS	Hela-S3	cervix
34	chr1:45258800-45259400	Enhancers	HepG2	liver
35	chr1:45258800-45259600	Enhancers	Esophagus	oesophagus

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