Variant report

Variant	rs1390401
Chromosome Location	chr1:227797950-227797951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227797816..227799614-chr1:227803015..227804639,2	MCF-7	breast:
2	chr1:227786695..227788345-chr1:227795346..227798093,2	K562	blood:
3	chr1:227797075..227799559-chr1:227811537..227814521,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225934	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1045407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753436	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753437	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799422	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799428	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799437	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799444	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10916154	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916157	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916160	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916161	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916162	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916163	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916166	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916167	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916173	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]
rs10916180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916189	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916199	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11576992	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11581704	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590390	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12058246	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12081818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084072	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12092054	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12093031	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12116848	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12120182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123996	0.90[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12129704	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12129894	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131114	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132761	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12133625	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12138198	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12138229	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140813	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140848	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495848	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1845757	0.85[EUR][1000 genomes]
rs1995019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172936	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446171	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999742	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34421331	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3942992	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4379651	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57158394	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61824940	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426470	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426471	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426472	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656661	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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659012	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669236	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669277	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6672530	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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678802	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679855	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689375	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692376	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694427	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696239	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];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698409	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74140304	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7418348	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7521812	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531801	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7538206	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538893	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540382	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7549475	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551788	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7553531	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903691	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951084	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9726691	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	18391952	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1390401	TAF5L	cis	parietal	SCAN
rs1390401	ZNF678	cis	cerebellum	SCAN
rs1390401	JMJD4	cis	multi-tissue	Pritchard

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227774800-227799200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:227774800-227805000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:227779200-227799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:227781200-227800800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:227784000-227798800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:227784000-227799600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:227790800-227801800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:227791000-227799600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:227791400-227798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:227791400-227798200	Weak transcription	Gastric	stomach
13	chr1:227791400-227799200	Weak transcription	Ovary	ovary
14	chr1:227791400-227799600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:227791400-227801000	Weak transcription	Psoas Muscle	Psoas
16	chr1:227792000-227798800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:227792400-227798000	Weak transcription	Fetal Lung	lung
18	chr1:227792600-227799600	Weak transcription	Thymus	Thymus
19	chr1:227792800-227798400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:227794400-227804400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:227794600-227798000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:227794600-227800000	Weak transcription	Right Ventricle	heart
23	chr1:227794600-227802000	Weak transcription	Placenta	Placenta
24	chr1:227794600-227808600	Weak transcription	Left Ventricle	heart
25	chr1:227795200-227801200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:227795200-227807000	Weak transcription	Fetal Heart	heart
27	chr1:227795400-227798200	Weak transcription	Primary B cells from cord blood	blood
28	chr1:227796200-227807200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:227796600-227798000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:227796600-227799600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:227796800-227801600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:227796800-227806000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:227797400-227799000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:227797400-227799800	Weak transcription	HSMMtube	muscle
35	chr1:227797400-227803400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:227797600-227799400	Weak transcription	Brain Substantia Nigra	brain
37	chr1:227797600-227804800	ZNF genes & repeats	Fetal Stomach	stomach
38	chr1:227797800-227798000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:227797800-227798000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:227797800-227798400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:227797800-227799200	Weak transcription	Fetal Intestine Large	intestine
42	chr1:227797800-227800400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:227797800-227800400	ZNF genes & repeats	Dnd41	blood
44	chr1:227797800-227804800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr1:227797800-227805800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
46	chr1:227797800-227806400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr1:227797800-227807200	ZNF genes & repeats	Fetal Brain Female	brain

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