Variant report

Variant	rs13125250
Chromosome Location	chr4:8010112-8010113
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	chr4:8008264..8010463-chr4:8011198..8013869,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163995	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1320076	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17180256	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[ASN][1000 genomes]
rs4696665	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6837516	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829851	chr4:7958698-8049060	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv878579	chr4:7969594-8011696	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv593623	chr4:7991587-8012167	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv829852	chr4:7991906-8151267	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7979600-8011400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:7986800-8011400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:7998600-8011600	Weak transcription	Fetal Brain Female	brain
4	chr4:7998800-8011800	Weak transcription	Fetal Intestine Small	intestine
5	chr4:8000000-8011200	Strong transcription	Spleen	Spleen
6	chr4:8003400-8011400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:8003400-8012000	Weak transcription	Gastric	stomach
8	chr4:8004800-8010600	Strong transcription	Brain Cingulate Gyrus	brain
9	chr4:8004800-8010800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:8005200-8010600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:8005200-8012200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:8006000-8010800	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr4:8006600-8011600	Weak transcription	Stomach Mucosa	stomach
14	chr4:8007200-8018000	Weak transcription	Psoas Muscle	Psoas
15	chr4:8007600-8010600	Weak transcription	Brain Germinal Matrix	brain
16	chr4:8007800-8011400	Weak transcription	Pancreas	Pancrea
17	chr4:8007800-8011600	Weak transcription	Brain Anterior Caudate	brain
18	chr4:8007800-8012200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:8007800-8022000	Weak transcription	Esophagus	oesophagus
20	chr4:8008000-8011600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:8008000-8011600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:8008600-8011400	Weak transcription	Fetal Brain Male	brain
23	chr4:8008600-8012000	Weak transcription	Fetal Heart	heart
24	chr4:8008600-8012400	Weak transcription	Right Ventricle	heart
25	chr4:8009000-8012400	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:8009200-8010600	Strong transcription	Left Ventricle	heart
27	chr4:8009200-8012200	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:8009400-8010600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:8009400-8012400	Weak transcription	Adipose Nuclei	Adipose
30	chr4:8009600-8010400	Strong transcription	Aorta	Aorta
31	chr4:8009600-8011400	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:8009600-8011400	Weak transcription	Fetal Stomach	stomach
33	chr4:8009800-8011400	Weak transcription	Brain Substantia Nigra	brain
34	chr4:8010000-8010600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:8010000-8011600	Weak transcription	Brain Angular Gyrus	brain
36	chr4:8010000-8012000	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links