Variant report

Variant	rs13220110
Chromosome Location	chr6:163686016-163686017
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	chr6:163684336..163687105-chr6:163835790..163838272,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12526405	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13190700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13192154	0.84[ASN][1000 genomes]
rs13192253	0.82[ASN][1000 genomes]
rs13192267	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13194634	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13194912	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13197790	0.84[ASN][1000 genomes]
rs13198111	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13200222	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13200354	0.84[ASN][1000 genomes]
rs13200617	0.83[ASN][1000 genomes]
rs13201846	0.84[ASN][1000 genomes]
rs13202006	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13202129	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13205335	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13209061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13214395	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13216996	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13217534	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13219871	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13219986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220528	0.84[ASN][1000 genomes]
rs13220802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233	0.82[ASN][1000 genomes]
rs6913469	0.88[EUR][1000 genomes];0.84[ASN][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	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1026490	chr6:163133433-163705708	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869286	chr6:163146342-163697445	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163680000-163686600	Enhancers	Fetal Heart	heart
2	chr6:163682000-163686200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:163682000-163686400	Enhancers	Brain Cingulate Gyrus	brain
4	chr6:163682000-163686400	Enhancers	Brain Substantia Nigra	brain
5	chr6:163682000-163701600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:163682200-163686600	Enhancers	Brain Hippocampus Middle	brain
7	chr6:163682600-163688000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:163682800-163686400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr6:163683200-163686400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:163683600-163686400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:163683800-163686400	Enhancers	Left Ventricle	heart
12	chr6:163684800-163686400	Enhancers	Right Ventricle	heart
13	chr6:163685000-163686600	Enhancers	Liver	Liver
14	chr6:163685200-163686400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:163685200-163686400	Enhancers	Pancreas	Pancrea
16	chr6:163685200-163686400	Enhancers	Stomach Mucosa	stomach
17	chr6:163685400-163686400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:163685400-163686400	Enhancers	Placenta	Placenta
19	chr6:163685400-163686400	Enhancers	Gastric	stomach
20	chr6:163685600-163686200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:163685800-163688200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr6:163686000-163686200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:163686000-163706000	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links