Variant report

Variant	rs62474003
Chromosome Location	chr7:112010650-112010651
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	NFIC	chr7:112010301-112011025	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr7:112010429-112011035	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112010041..112012440-chr7:112089229..112091559,2	MCF-7	breast:

Variant related genes	Relation type
MTND5P8	TF binding region
ENSG00000236232	TF binding region
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs2006275	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2016864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2396531	1.00[EUR][1000 genomes]
rs2396532	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4425678	1.00[EUR][1000 genomes]
rs62473060	0.92[AMR][1000 genomes]
rs62473127	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62473129	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62473137	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62473139	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62473141	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62473143	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62473145	1.00[EUR][1000 genomes]
rs62473146	1.00[EUR][1000 genomes]
rs62473147	1.00[EUR][1000 genomes]
rs62473148	1.00[EUR][1000 genomes]
rs62473149	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62473150	1.00[EUR][1000 genomes]
rs62473152	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62473153	1.00[EUR][1000 genomes]
rs62473154	1.00[EUR][1000 genomes]
rs62473156	1.00[EUR][1000 genomes]
rs62473157	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62473960	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62474000	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62474001	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62474007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62474009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62474010	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62474011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62474012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62474014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6960155	1.00[EUR][1000 genomes]
rs6971079	1.00[EUR][1000 genomes]
rs73440635	0.85[AMR][1000 genomes]
rs736760	1.00[EUR][1000 genomes]
rs739746	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532335	chr7:111411990-112054905	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
3	nsv1020212	chr7:111944370-112032596	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:111999600-112010800	Weak transcription	Right Atrium	heart
2	chr7:112010000-112011400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:112010000-112011800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr7:112010600-112011000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr7:112010600-112011200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:112010600-112011200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:112010600-112011400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr7:112010600-112011400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:112010600-112011800	Enhancers	Fetal Lung	lung
10	chr7:112010600-112012000	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links