Variant report

Variant	rs12405750
Chromosome Location	chr1:209977844-209977845
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	chr1:209977100-209978010	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:209975033-209981799	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209976817..209979056-chr1:209982865..209985197,2	K562	blood:
2	chr1:209977687..209979481-chr1:210546829..210548447,2	MCF-7	breast:
3	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
4	chr1:209956472..209958097-chr1:209976209..209979148,2	MCF-7	breast:

Variant related genes	Relation type
IRF6	TF binding region
ENSG00000232222	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10489343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779514	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863790	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1109430	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119345	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11119346	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119360	1.00[AFR][1000 genomes]
rs11585733	1.00[AFR][1000 genomes]
rs11589335	1.00[AFR][1000 genomes]
rs12058100	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes]
rs12063989	1.00[AFR][1000 genomes]
rs12064085	1.00[AFR][1000 genomes]
rs12064211	1.00[AFR][1000 genomes]
rs12064398	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12066340	1.00[AFR][1000 genomes]
rs12069187	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12075674	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12080691	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12081405	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12083685	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12561766	1.00[AFR][1000 genomes]
rs12563527	1.00[AFR][1000 genomes]
rs12566152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015217	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015255	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015268	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1856161	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883332	1.00[AFR][1000 genomes]
rs2038053	1.00[AFR][1000 genomes]
rs2069068	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076149	1.00[AFR][1000 genomes]
rs2076151	1.00[AFR][1000 genomes]
rs2142860	1.00[AFR][1000 genomes]
rs2235370	0.85[AMR][1000 genomes]
rs2235371	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235377	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272866	1.00[AFR][1000 genomes]
rs2282740	1.00[AFR][1000 genomes]
rs3753517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274836	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4140636	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4329516	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4844491	1.00[AFR][1000 genomes]
rs4844494	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844496	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4844893	1.00[AFR][1000 genomes]
rs4844894	1.00[AFR][1000 genomes]
rs4844908	1.00[AFR][1000 genomes]
rs57283682	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
4	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:209964200-209978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:209964400-209978200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:209966000-209978000	Weak transcription	Colonic Mucosa	Colon
8	chr1:209966000-209978400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:209969000-209978600	Weak transcription	Lung	lung
10	chr1:209972000-209978400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:209972000-209978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:209974200-209978200	Transcr. at gene 5' and 3'	HMEC	breast
13	chr1:209974200-209978800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:209974600-209978000	Enhancers	Pancreas	Pancrea
15	chr1:209974600-209978200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:209974800-209979000	Transcr. at gene 5' and 3'	NHEK	skin
17	chr1:209975600-209978400	Enhancers	Liver	Liver
18	chr1:209975600-209979200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:209975600-209979200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:209975800-209978200	Enhancers	Fetal Heart	heart
21	chr1:209975800-209979200	Weak transcription	Aorta	Aorta
22	chr1:209976000-209978000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:209977000-209978600	Weak transcription	Right Atrium	heart
24	chr1:209977000-209978600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:209977000-209980000	Active TSS	Esophagus	oesophagus
26	chr1:209977200-209978000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:209977400-209978200	Enhancers	Placenta	Placenta
28	chr1:209977400-209979800	Active TSS	Duodenum Mucosa	Duodenum
29	chr1:209977600-209978000	Flanking Active TSS	Fetal Intestine Small	intestine
30	chr1:209977600-209978000	Enhancers	Stomach Mucosa	stomach
31	chr1:209977600-209978200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
32	chr1:209977600-209978200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr1:209977600-209979400	Weak transcription	HSMMtube	muscle
34	chr1:209977600-209980200	Flanking Active TSS	HUVEC	blood vessel
35	chr1:209977800-209978000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:209977800-209978400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr1:209977800-209978400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr1:209977800-209979200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:209977800-209979200	Bivalent/Poised TSS	Fetal Thymus	thymus
40	chr1:209977800-209979400	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr1:209977800-209979600	Active TSS	Fetal Intestine Large	intestine
42	chr1:209977800-209979600	Active TSS	Gastric	stomach
43	chr1:209977800-209980000	Active TSS	Rectal Smooth Muscle	rectum
44	chr1:209977800-209980200	Active TSS	Pancreatic Islets	Pancreatic Islet

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