Variant report

Variant	rs72929299
Chromosome Location	chr1:70824629-70824630
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	POU2F2	chr1:70824610-70825221	GM12878	blood:	n/a	n/a
2	EP300	chr1:70824623-70825373	GM12878	blood:	n/a	chr1:70824960-70824968
3	RUNX3	chr1:70824604-70825353	GM12878	blood:	n/a	n/a
4	RUNX3	chr1:70824513-70825457	GM12878	blood:	n/a	n/a
5	NFIC	chr1:70824544-70825448	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70819013..70822302-chr1:70824014..70829303,9	MCF-7	breast:

Variant related genes	Relation type
ANKRD13C	TF binding region
ENSG00000118454	Chromatin interaction
ENSG00000197568	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10889867	0.86[AFR][1000 genomes]
rs56688715	1.00[AMR][1000 genomes]
rs57480626	1.00[AFR][1000 genomes]
rs57627286	1.00[AMR][1000 genomes]
rs57928672	1.00[AMR][1000 genomes]
rs59856193	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61084750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61493071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72917819	1.00[AMR][1000 genomes]
rs72917823	1.00[AMR][1000 genomes]
rs72921081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72929203	1.00[AMR][1000 genomes]
rs72929206	1.00[AMR][1000 genomes]
rs72929207	1.00[AMR][1000 genomes]
rs72929211	1.00[AMR][1000 genomes]
rs72929214	1.00[AMR][1000 genomes]
rs72929215	1.00[AMR][1000 genomes]
rs72929225	1.00[AMR][1000 genomes]
rs72929226	1.00[AMR][1000 genomes]
rs72929228	1.00[AMR][1000 genomes]
rs72929237	1.00[AMR][1000 genomes]
rs72929241	1.00[AMR][1000 genomes]
rs72929267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72929270	1.00[AFR][1000 genomes]
rs72929272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72929274	1.00[AFR][1000 genomes]
rs72929275	1.00[AFR][1000 genomes]
rs72929277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72929286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72929291	1.00[AFR][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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	esv11736	chr1:70820591-70825114	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	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	chr1:70821000-70827600	Weak transcription	HSMM	muscle
2	chr1:70821000-70835200	Weak transcription	Pancreas	Pancrea
3	chr1:70821000-70836400	Weak transcription	Left Ventricle	heart
4	chr1:70821000-70838400	Weak transcription	Lung	lung
5	chr1:70821200-70827600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:70821200-70828000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:70821200-70829600	Weak transcription	Fetal Intestine Small	intestine
8	chr1:70821200-70832000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:70821200-70833600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:70821200-70835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:70821200-70836800	Weak transcription	Fetal Stomach	stomach
12	chr1:70821200-70841400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:70821400-70827000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:70821400-70827400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:70821400-70827400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:70821400-70827600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:70821400-70827600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:70821400-70827600	Weak transcription	Fetal Lung	lung
19	chr1:70821400-70827800	Weak transcription	Small Intestine	intestine
20	chr1:70821400-70832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:70821400-70832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:70821400-70838000	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:70821600-70828200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:70821600-70834800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:70821600-70836400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:70821600-70839000	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:70822000-70827400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:70822000-70827600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:70822000-70827600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:70822000-70829000	Weak transcription	Brain Anterior Caudate	brain
31	chr1:70822000-70834000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:70822000-70836400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:70822000-70839400	Weak transcription	Brain Substantia Nigra	brain
34	chr1:70822200-70829400	Weak transcription	K562	blood
35	chr1:70822200-70835600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:70822400-70834600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:70823400-70827200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:70824000-70825000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:70824000-70825800	Enhancers	GM12878-XiMat	blood
40	chr1:70824200-70826000	Enhancers	HMEC	breast
41	chr1:70824400-70826200	Enhancers	NHEK	skin
42	chr1:70824600-70824800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:70824600-70825000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:70824600-70825800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links