Variant report

Variant	rs6078922
Chromosome Location	chr20:13100629-13100630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:12905650..12906529-chr20:13100262..13100853,2	MCF-7	breast:
2	chr20:13099864..13101163-chr20:13242113..13243382,13	MCF-7	breast:
3	chr20:13100265..13100795-chr20:13526790..13527749,2	MCF-7	breast:
4	chr20:12950887..12951603-chr20:13099913..13100746,2	MCF-7	breast:
5	chr20:13099915..13100786-chr20:13283022..13283937,3	MCF-7	breast:
6	chr20:13099895..13100678-chr20:13283242..13284334,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12625162	0.93[CHB][hapmap]
rs12625797	0.89[CHB][hapmap]
rs13042895	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2180365	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2208004	0.95[CHB][hapmap]
rs2236125	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2236126	0.82[ASN][1000 genomes]
rs2327752	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2327753	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35868902	0.80[ASN][1000 genomes]
rs4274654	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs6033620	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6041857	0.89[CHB][hapmap]
rs6074558	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6074559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074560	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs6074561	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.90[ASN][1000 genomes]
rs6078920	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6078925	0.92[CHB][hapmap];0.89[ASN][1000 genomes]
rs6078926	0.89[ASN][1000 genomes]
rs6105040	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109701	0.87[CHB][hapmap]
rs6109703	0.89[CHB][hapmap]
rs6109704	0.94[CHB][hapmap]
rs6109717	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs845727	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv833924	chr20:12997093-13189239	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13049600-13121800	Weak transcription	Primary T cells from cord blood	blood
2	chr20:13049800-13117600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:13071600-13108000	Weak transcription	Left Ventricle	heart
4	chr20:13073400-13101400	Weak transcription	Fetal Muscle Leg	muscle
5	chr20:13080800-13102400	Weak transcription	Thymus	Thymus
6	chr20:13083600-13114600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr20:13086200-13107600	Weak transcription	NHEK	skin
8	chr20:13086600-13123200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:13087000-13108200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr20:13087200-13101600	Strong transcription	Placenta	Placenta
11	chr20:13087800-13107200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr20:13088800-13103000	Strong transcription	Fetal Intestine Large	intestine
13	chr20:13091800-13127800	Weak transcription	Fetal Kidney	kidney
14	chr20:13093000-13144600	Weak transcription	Pancreas	Pancrea
15	chr20:13093200-13102600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr20:13093200-13106800	Weak transcription	Ovary	ovary
17	chr20:13093400-13108000	Weak transcription	Aorta	Aorta
18	chr20:13093400-13111000	Weak transcription	Lung	lung
19	chr20:13094200-13103400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr20:13094600-13114400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:13094800-13101800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr20:13096600-13116600	Weak transcription	Right Ventricle	heart
23	chr20:13098400-13107200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr20:13098600-13101400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:13098600-13105200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:13098800-13101200	Weak transcription	Fetal Intestine Small	intestine
27	chr20:13099400-13102200	Weak transcription	Liver	Liver
28	chr20:13100000-13103600	Genic enhancers	HepG2	liver
29	chr20:13100000-13108800	Weak transcription	Adipose Nuclei	Adipose
30	chr20:13100400-13102200	Enhancers	Fetal Lung	lung
31	chr20:13100600-13101000	Weak transcription	Fetal Stomach	stomach
32	chr20:13100600-13101400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr20:13100600-13101400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr20:13100600-13103000	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links