Variant report

Variant	rs12778832
Chromosome Location	chr10:5657229-5657230
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr10:5657198-5657523	HepG2	liver:	n/a	n/a
2	FOXA2	chr10:5657085-5657664	A549	lung:	n/a	n/a
3	FOXA2	chr10:5657059-5657706	A549	lung:	n/a	n/a
4	TCF12	chr10:5657030-5657687	A549	lung:	n/a	n/a
5	FOXA1	chr10:5657161-5657550	HepG2	liver:	n/a	n/a
6	FOXA1	chr10:5657189-5657538	HepG2	liver:	n/a	n/a
7	FOXA1	chr10:5657149-5657602	HepG2	liver:	n/a	n/a
8	FOXA1	chr10:5657185-5657487	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:5487123..5488700-chr10:5656532..5659237,2	K562	blood:
2	chr10:5484376..5493176-chr10:5653017..5671828,35	MCF-7	breast:
3	chr10:5650796..5653722-chr10:5656355..5659325,2	MCF-7	breast:
4	chr10:5643461..5645652-chr10:5657052..5659260,2	MCF-7	breast:
5	chr10:5529812..5532374-chr10:5655827..5658800,2	MCF-7	breast:
6	chr10:5594983..5597164-chr10:5655086..5657673,2	MCF-7	breast:
7	chr10:5506585..5509485-chr10:5655712..5657765,3	MCF-7	breast:
8	chr10:5483715..5496703-chr10:5653374..5669304,43	MCF-7	breast:
9	chr10:5655010..5657602-chr10:5662784..5666424,4	MCF-7	breast:
10	chr10:5655720..5657948-chr10:5668389..5670960,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231483	TF binding region
ENSG00000231483	Chromatin interaction
ENSG00000173848	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10795569	0.95[EUR][1000 genomes]
rs10795575	0.94[EUR][1000 genomes]
rs10795585	0.94[EUR][1000 genomes]
rs11594094	0.90[EUR][1000 genomes]
rs12250399	0.94[EUR][1000 genomes]
rs12266655	0.94[EUR][1000 genomes]
rs12765374	0.81[AMR][1000 genomes]
rs12771305	0.91[EUR][1000 genomes]
rs4747436	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4750462	0.81[AMR][1000 genomes]
rs4750485	0.81[AMR][1000 genomes]
rs7098582	0.81[AMR][1000 genomes]
rs7896428	0.81[AMR][1000 genomes]
rs7917232	0.81[AMR][1000 genomes]
rs9663617	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv894798	chr10:5503610-5670275	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv523491	chr10:5542109-5720067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	esv2757364	chr10:5557024-5720512	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1040932	chr10:5637870-5665774	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv466718	chr10:5639907-5657527	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv549890	chr10:5639907-5657527	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv894806	chr10:5643511-5670275	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1054888	chr10:5645033-5694612	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv466719	chr10:5645895-5662915	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv549891	chr10:5645895-5662915	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv519582	chr10:5646103-5720067	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv894807	chr10:5647942-5691135	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv8599	chr10:5649129-5719928	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv1050965	chr10:5649760-5717125	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
19	nsv1044330	chr10:5652006-5717125	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	22 gene(s)	inside rSNPs	diseases
20	nsv975791	chr10:5652225-5711077	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
21	nsv466720	chr10:5652277-5715401	Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
22	nsv549892	chr10:5652277-5715401	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases
23	nsv1037709	chr10:5652739-5717125	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases
24	nsv470917	chr10:5654167-5715401	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
25	nsv818742	chr10:5654167-5715401	Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
26	nsv1036492	chr10:5656962-5711147	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
27	nsv540473	chr10:5656962-5711147	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases
28	nsv1036253	chr10:5657162-5711008	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
29	nsv540474	chr10:5657162-5711008	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
30	esv3409277	chr10:5657171-5659719	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5649000-5657400	Weak transcription	Left Ventricle	heart
2	chr10:5650200-5662600	Enhancers	Fetal Muscle Leg	muscle
3	chr10:5650400-5661800	Enhancers	Fetal Muscle Trunk	muscle
4	chr10:5651800-5665000	Weak transcription	Spleen	Spleen
5	chr10:5652200-5660800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr10:5652200-5660800	Weak transcription	Right Ventricle	heart
7	chr10:5652800-5658600	Enhancers	HMEC	breast
8	chr10:5653400-5657400	Weak transcription	Psoas Muscle	Psoas
9	chr10:5655600-5657600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr10:5655600-5658000	Enhancers	Placenta	Placenta
11	chr10:5655600-5658800	Enhancers	Stomach Smooth Muscle	stomach
12	chr10:5655800-5658000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr10:5655800-5658200	Enhancers	NHDF-Ad	bronchial
14	chr10:5656000-5665000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr10:5656200-5657600	Weak transcription	Fetal Thymus	thymus
16	chr10:5656400-5657600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr10:5656400-5658800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:5656400-5660000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:5656400-5660200	Weak transcription	Right Atrium	heart
20	chr10:5656400-5660800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:5656400-5661200	Weak transcription	Fetal Kidney	kidney
22	chr10:5656600-5657600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:5656600-5657600	Weak transcription	Colonic Mucosa	Colon
24	chr10:5656600-5657800	Weak transcription	Ovary	ovary
25	chr10:5656600-5657800	Enhancers	Hela-S3	cervix
26	chr10:5656600-5658000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:5656600-5658000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:5656600-5658000	Weak transcription	Esophagus	oesophagus
29	chr10:5656600-5658600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr10:5656600-5658800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:5656600-5658800	Weak transcription	Pancreas	Pancrea
32	chr10:5656600-5658800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr10:5656600-5659000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:5656600-5659000	Weak transcription	NHEK	skin
35	chr10:5656600-5659000	Enhancers	Osteobl	bone
36	chr10:5656600-5659800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:5656600-5660000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr10:5656600-5660000	Enhancers	HepG2	liver
39	chr10:5656600-5660400	Weak transcription	Fetal Intestine Large	intestine
40	chr10:5656600-5661000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr10:5656600-5661000	Weak transcription	Fetal Lung	lung
42	chr10:5656600-5661000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr10:5656600-5661000	Weak transcription	Stomach Mucosa	stomach
44	chr10:5656600-5661200	Weak transcription	NHLF	lung
45	chr10:5656600-5661400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr10:5656600-5662800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr10:5656600-5665000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr10:5656600-5665000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr10:5656800-5659400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr10:5656800-5661000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links