Variant report

Variant	rs12654995
Chromosome Location	chr5:177663493-177663494
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr5:177663488-177663985	HepG2	liver:	n/a	n/a
2	WRNIP1	chr5:177663426-177663538	GM12878	blood:	n/a	n/a
3	STAT3	chr5:177663488-177663688	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:177663268-177665103	HL-60	blood:	n/a	n/a
5	POLR2A	chr5:177663195-177665265	HL-60	blood:	n/a	n/a
6	RCOR1	chr5:177663389-177663849	K562	blood:	n/a	n/a
7	BHLHE40	chr5:177663448-177664079	K562	blood:	n/a	n/a
8	NR2F2	chr5:177663454-177664090	MCF-7	breast:	n/a	n/a
9	MAZ	chr5:177663454-177663979	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:177663359..177666352-chr5:177692543..177695366,2	K562	blood:
2	chr5:177663150..177665160-chr5:178157825..178159335,2	MCF-7	breast:
3	chr5:177662961..177665111-chr5:178052520..178054523,2	MCF-7	breast:

No data

Variant related genes	Relation type
PHYKPL	TF binding region
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs4045767	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59187144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62388742	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62388744	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	106 gene(s)	inside rSNPs	diseases
5	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
7	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
8	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1018031	chr5:177655010-177746378	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv537969	chr5:177655010-177746378	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv883195	chr5:177655194-177690539	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	nsv883196	chr5:177655194-177690978	Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv883197	chr5:177655194-177707204	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	nsv1025291	chr5:177657927-177756215	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv537970	chr5:177657927-177756215	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	nsv527792	chr5:177659075-177675217	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv883198	chr5:177659075-177690539	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
18	nsv883199	chr5:177661902-177717640	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177659800-177665800	Weak transcription	Gastric	stomach
2	chr5:177660000-177663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:177660000-177664600	Weak transcription	Small Intestine	intestine
4	chr5:177660200-177664600	Weak transcription	HSMM	muscle
5	chr5:177660200-177665200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:177660200-177665800	Enhancers	Primary T cells fromperipheralblood	blood
7	chr5:177660200-177667000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr5:177660200-177667000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:177660200-177667600	Enhancers	Fetal Muscle Trunk	muscle
10	chr5:177660400-177663600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:177660400-177663600	Weak transcription	Brain Angular Gyrus	brain
12	chr5:177660400-177663600	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:177660400-177663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:177660400-177663600	Weak transcription	Osteobl	bone
15	chr5:177660400-177663800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:177660400-177663800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:177660400-177664000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:177660400-177664000	Weak transcription	Fetal Intestine Small	intestine
19	chr5:177660400-177664200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:177660400-177664200	Weak transcription	Esophagus	oesophagus
21	chr5:177660400-177664200	Weak transcription	HSMMtube	muscle
22	chr5:177660400-177664400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:177660400-177664600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr5:177660400-177665800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:177660400-177665800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:177660400-177666200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:177660400-177668000	Enhancers	Primary hematopoietic stem cells	blood
28	chr5:177660600-177664400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:177660600-177664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:177661200-177664400	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr5:177661200-177666400	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr5:177661400-177666200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr5:177661400-177667800	Enhancers	Adipose Nuclei	Adipose
34	chr5:177661400-177669600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr5:177661600-177666400	Enhancers	Fetal Muscle Leg	muscle
36	chr5:177661600-177671600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:177661800-177663600	Weak transcription	HMEC	breast
38	chr5:177661800-177665400	Enhancers	Spleen	Spleen
39	chr5:177661800-177666400	Enhancers	Duodenum Mucosa	Duodenum
40	chr5:177661800-177666600	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr5:177661800-177667600	Enhancers	Liver	Liver
42	chr5:177661800-177669800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr5:177662000-177663800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:177662000-177665600	Enhancers	Pancreas	Pancrea
45	chr5:177662200-177663600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr5:177662200-177663800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:177662200-177664000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr5:177662200-177664000	Weak transcription	Fetal Intestine Large	intestine
49	chr5:177662200-177664000	Weak transcription	Placenta	Placenta
50	chr5:177662200-177664200	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links