Variant report

Variant	rs12034454
Chromosome Location	chr1:171754436-171754437
allele	A/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	STAT3	chr1:171754411-171754917	MCF10A-Er-Src	breast:	n/a	chr1:171754502-171754509

No.	Distal block	Cell Line	Cell type
1	chr1:171712949..171715185-chr1:171753608..171756289,2	K562	blood:
2	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
3	chr1:171754075..171756411-chr1:171764040..171766145,2	MCF-7	breast:

Variant related genes	Relation type
METTL13	TF binding region
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10798634	0.84[EUR][1000 genomes]
rs10798636	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10798667	0.92[ASN][1000 genomes]
rs10798692	0.83[MEX][hapmap]
rs10913644	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11587288	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11803889	0.89[YRI][hapmap]
rs12028128	0.84[EUR][1000 genomes]
rs12032340	0.82[MEX][hapmap];0.84[EUR][1000 genomes]
rs12039034	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12566700	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.93[ASN][1000 genomes]
rs16843385	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232818	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232826	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294723	0.83[MEX][hapmap]
rs3753538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56178029	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57476157	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59302445	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60502293	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60956160	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6425405	0.84[EUR][1000 genomes]
rs6425423	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425438	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs6425439	0.91[ASN][1000 genomes]
rs6684594	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6690544	0.86[LWK][hapmap];0.89[YRI][hapmap]
rs6691222	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6692136	0.84[EUR][1000 genomes]
rs6695502	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72703115	0.92[ASN][1000 genomes]
rs7541192	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7542116	0.84[EUR][1000 genomes]
rs7543608	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7548462	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551037	0.83[EUR][1000 genomes]
rs7860	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909958	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941942	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv522889	chr1:171749665-171755071	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv518222	chr1:171753039-171763549	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751400-171755000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:171751600-171754800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:171752000-171754600	Weak transcription	HSMMtube	muscle
5	chr1:171752000-171754800	Weak transcription	Small Intestine	intestine
6	chr1:171752000-171755000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:171752200-171755000	Weak transcription	Osteobl	bone
9	chr1:171752200-171759200	Weak transcription	Fetal Heart	heart
10	chr1:171752200-171762200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:171752200-171766600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:171752200-171767400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:171752200-171768200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:171752400-171754800	Genic enhancers	Duodenum Mucosa	Duodenum
15	chr1:171752400-171754800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:171752400-171754800	Weak transcription	HUVEC	blood vessel
17	chr1:171752400-171755400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:171752400-171755400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:171752400-171755400	Genic enhancers	K562	blood
20	chr1:171752400-171755600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:171752400-171766600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:171752400-171767200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:171752600-171754600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:171752600-171754600	Genic enhancers	Liver	Liver
25	chr1:171752600-171754600	Strong transcription	HSMM	muscle
26	chr1:171752600-171755000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:171752600-171755200	Genic enhancers	Stomach Smooth Muscle	stomach
28	chr1:171752600-171755600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:171752600-171756400	Strong transcription	NHEK	skin
30	chr1:171752600-171760000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:171752600-171767000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:171752600-171767000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:171752600-171767400	Strong transcription	Primary B cells from cord blood	blood
34	chr1:171752600-171767400	Strong transcription	A549	lung
35	chr1:171752600-171767800	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr1:171752600-171767800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:171752800-171754600	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr1:171752800-171754800	Genic enhancers	Fetal Brain Female	brain
39	chr1:171752800-171755400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:171752800-171755400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr1:171752800-171755400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:171752800-171755400	Genic enhancers	Lung	lung
43	chr1:171752800-171755600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:171752800-171755800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:171752800-171756000	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr1:171752800-171756000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:171752800-171757200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:171752800-171757800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:171752800-171761800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:171752800-171762600	Strong transcription	Fetal Stomach	stomach

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