Variant report

Variant	rs2007148
Chromosome Location	chr1:179850543-179850544
allele	C/G
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	chr1:179850484-179852590	HUVEC	blood vessel:	n/a	n/a
2	NR2F2	chr1:179850416-179853079	K562	blood:	n/a	n/a
3	EP300	chr1:179850371-179852139	GM12878	blood:	n/a	chr1:179851495-179851504 chr1:179851177-179851190
4	BRCA1	chr1:179850535-179852341	Hela-S3	cervix:	n/a	n/a
5	IRF1	chr1:179850326-179852180	K562	blood:	n/a	chr1:179851146-179851159 chr1:179851146-179851160 chr1:179851145-179851159 chr1:179851146-179851158
6	JUN	chr1:179850203-179853448	K562	blood:	n/a	chr1:179852958-179852967 chr1:179853052-179853060 chr1:179852986-179852994 chr1:179852982-179852993
7	MYC	chr1:179850287-179852395	K562	blood:	n/a	n/a
8	TBP	chr1:179850526-179852145	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:179850422-179853318	GM12878	blood:	n/a	n/a
10	ARID3A	chr1:179850320-179852316	HepG2	liver:	n/a	chr1:179850758-179850774
11	EP300	chr1:179850534-179852172	K562	blood:	n/a	chr1:179851495-179851504 chr1:179851177-179851190
12	POLR2A	chr1:179850387-179853379	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:179850352-179852159	K562	blood:	n/a	n/a
14	POLR2A	chr1:179850540-179852516	PBDE	blood:	n/a	n/a
15	POLR2A	chr1:179850381-179853322	GM12891	blood:	n/a	n/a
16	POLR2A	chr1:179850471-179852506	IMR90	lung:	n/a	n/a
17	POLR2A	chr1:179850482-179852461	K562	blood:	n/a	n/a
18	NRF1	chr1:179850517-179852001	Hela-S3	cervix:	n/a	chr1:179851759-179851770
19	TEAD4	chr1:179850427-179852228	K562	blood:	n/a	n/a
20	MAZ	chr1:179850360-179852536	IMR90	lung:	n/a	n/a
21	HCFC1	chr1:179850184-179853343	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:179850386-179852251	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr1:179850416-179853104	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179848142..179854405-chr1:179919774..179927189,17	MCF-7	breast:
2	chr1:179833317..179835863-chr1:179849395..179853272,4	MCF-7	breast:
3	chr1:179849806..179852481-chr17:56735365..56738310,2	MCF-7	breast:
4	chr1:179849600..179851970-chr1:180040830..180043217,3	K562	blood:
5	chr1:179850426..179852030-chr1:179871802..179874421,2	MCF-7	breast:
6	chr1:179849468..179853023-chr1:180122560..180126275,4	K562	blood:
7	chr1:179849896..179853295-chr1:179868800..179873439,8	K562	blood:
8	chr1:179850318..179852494-chr17:27276905..27279440,2	MCF-7	breast:
9	chr1:179849016..179853452-chr1:179922333..179928502,16	K562	blood:
10	chr1:179850058..179853356-chr1:179869131..179876291,8	K562	blood:
11	chr1:179850172..179852530-chr1:180041069..180043217,2	K562	blood:
12	chr1:179847679..179853408-chr1:179922379..179926886,15	MCF-7	breast:
13	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:

Variant related genes	Relation type
TOR1AIP2	TF binding region
TOR1AIP1	TF binding region
ENSG00000135837	Chromatin interaction
ENSG00000264916	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000109118	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000179761	Chromatin interaction
ENSG00000258664	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1014394	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1144575	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1148812	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1148815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1148817	0.82[EUR][1000 genomes]
rs12062341	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12062383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1281378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1281408	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1281410	0.81[EUR][1000 genomes]
rs1281411	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1281412	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1281413	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1281428	0.94[ASN][1000 genomes]
rs1281429	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1281430	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1281432	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1298477	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1298479	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1300068	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245425	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249346	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2762858	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777908	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777909	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777917	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2794582	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2794583	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs474258	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs475233	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs475434	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs479094	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480377	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480498	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486906	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs501300	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs502036	0.84[CHD][hapmap];0.82[AMR][1000 genomes]
rs505789	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs505837	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs507603	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs514421	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs518774	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs522534	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs530369	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs530854	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs531814	0.82[CEU][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs538512	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs547776	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs549650	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs553830	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs555270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs555526	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs589780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs599185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600046	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600553	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs605807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609521	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612215	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs644412	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6657364	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	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
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv518936	chr1:179847402-179858333	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2007148	MRPS14	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179847000-179850800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:179847200-179850600	Weak transcription	Fetal Thymus	thymus
3	chr1:179847200-179850800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:179847200-179851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:179847200-179851000	Weak transcription	Gastric	stomach
6	chr1:179847200-179851000	Weak transcription	Lung	lung
7	chr1:179847400-179850600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:179847400-179850600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:179847400-179850600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:179847400-179850600	Weak transcription	Brain Germinal Matrix	brain
11	chr1:179847400-179850600	Weak transcription	Colonic Mucosa	Colon
12	chr1:179847400-179850600	Weak transcription	Fetal Brain Female	brain
13	chr1:179847400-179850600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:179847400-179850600	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:179847400-179850600	Weak transcription	Fetal Stomach	stomach
16	chr1:179847400-179850600	Weak transcription	Psoas Muscle	Psoas
17	chr1:179847400-179850600	Weak transcription	Thymus	Thymus
18	chr1:179847400-179850800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:179847400-179850800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:179847400-179850800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:179847400-179850800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:179847400-179850800	Weak transcription	Placenta	Placenta
23	chr1:179847400-179850800	Weak transcription	Left Ventricle	heart
24	chr1:179847400-179850800	Weak transcription	Ovary	ovary
25	chr1:179847400-179850800	Weak transcription	Pancreas	Pancrea
26	chr1:179847400-179851000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:179847400-179851000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:179847400-179851000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:179847400-179851000	Weak transcription	Small Intestine	intestine
30	chr1:179847400-179851000	Weak transcription	Spleen	Spleen
31	chr1:179847600-179850600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:179848000-179850600	Weak transcription	Stomach Mucosa	stomach
33	chr1:179849400-179853400	Active TSS	K562	blood
34	chr1:179849800-179850600	Enhancers	Primary T cells from cord blood	blood
35	chr1:179849800-179850600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:179849800-179850600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:179849800-179850600	Enhancers	Fetal Heart	heart
38	chr1:179849800-179850800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:179849800-179851200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:179849800-179853200	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr1:179850000-179850800	Active TSS	HepG2	liver
42	chr1:179850200-179851000	Flanking Active TSS	Hela-S3	cervix
43	chr1:179850200-179851000	Flanking Active TSS	Osteobl	bone
44	chr1:179850200-179852800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:179850200-179853200	Active TSS	NHEK	skin
46	chr1:179850200-179853600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:179850200-179853600	Active TSS	HMEC	breast
48	chr1:179850400-179850600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:179850400-179850600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:179850400-179850600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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