Variant report

Variant	rs12120308
Chromosome Location	chr1:224394909-224394910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224369572..224371706-chr1:224393451..224396309,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10799491	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10799507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10799543	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916414	0.80[AMR][1000 genomes]
rs10916458	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916462	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916472	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916481	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916497	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916498	0.85[EUR][1000 genomes]
rs12082619	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083770	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124547	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126765	0.84[EUR][1000 genomes]
rs12126815	0.80[EUR][1000 genomes]
rs12133599	0.92[EUR][1000 genomes]
rs12138866	0.88[EUR][1000 genomes]
rs12140137	0.96[EUR][1000 genomes]
rs12184283	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45583539	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60256604	0.84[EUR][1000 genomes]
rs6660194	0.92[EUR][1000 genomes]
rs6686449	0.96[EUR][1000 genomes]
rs6701036	0.85[EUR][1000 genomes]
rs68073536	0.85[EUR][1000 genomes]
rs72753956	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72753969	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72753980	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72753994	0.92[EUR][1000 genomes]
rs72754000	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72754001	0.88[EUR][1000 genomes]
rs72755905	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7514140	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7552239	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][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	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12120308	CNIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224391600-224400000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:224391600-224400200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:224391600-224407000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:224392600-224400400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:224392800-224395000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:224393400-224395200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:224393400-224399000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:224393600-224397000	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:224393600-224397200	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:224393600-224397400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:224393600-224397600	Weak transcription	Left Ventricle	heart
13	chr1:224393600-224397600	Weak transcription	Spleen	Spleen
14	chr1:224393600-224397800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:224393600-224397800	Weak transcription	Right Ventricle	heart
16	chr1:224393600-224398800	Weak transcription	Brain Substantia Nigra	brain
17	chr1:224393600-224398800	Weak transcription	Fetal Kidney	kidney
18	chr1:224393600-224399000	Weak transcription	Brain Anterior Caudate	brain
19	chr1:224393600-224399000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:224393600-224399000	Weak transcription	Psoas Muscle	Psoas
21	chr1:224393600-224399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:224393600-224399200	Weak transcription	Lung	lung
23	chr1:224393600-224400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:224393600-224400200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:224393600-224400200	Weak transcription	Gastric	stomach
26	chr1:224393600-224400400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:224393600-224400400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:224393600-224400800	Weak transcription	Right Atrium	heart
29	chr1:224393600-224401200	Weak transcription	Esophagus	oesophagus
30	chr1:224393600-224401200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:224393800-224395000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr1:224393800-224396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:224393800-224397200	Weak transcription	GM12878-XiMat	blood
34	chr1:224393800-224397800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:224393800-224398000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:224393800-224398000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:224393800-224398600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:224393800-224398800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:224393800-224398800	Weak transcription	Fetal Heart	heart
40	chr1:224393800-224398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:224393800-224398800	Weak transcription	Fetal Lung	lung
42	chr1:224393800-224398800	Weak transcription	Fetal Stomach	stomach
43	chr1:224393800-224399000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:224393800-224399000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:224393800-224399000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:224393800-224399000	Weak transcription	NH-A	brain
47	chr1:224393800-224399200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:224393800-224400200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:224393800-224400200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:224393800-224400200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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