Variant report

Variant	rs6792525
Chromosome Location	chr3:48590517-48590518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48589258-48590593	A549	lung:	n/a	n/a
2	POLR2A	chr3:48588992-48602017	U87	brain:	n/a	n/a
3	E2F6	chr3:48589878-48590546	H1-hESC	embryonic stem cell:	n/a	chr3:48590260-48590272
4	POLR2A	chr3:48590375-48590682	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:48590481-48590942	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:48589038-48592203	U87	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48580876..48582431-chr3:48589920..48591706,2	K562	blood:
2	chr3:48588342..48591266-chr3:48591852..48595141,3	K562	blood:
3	chr3:48507478..48509735-chr3:48590066..48592443,2	MCF-7	breast:
4	chr3:48585643..48588285-chr3:48588795..48591125,3	K562	blood:
5	chr3:48585238..48588232-chr3:48588632..48591166,3	MCF-7	breast:
6	chr3:48228246..48230030-chr3:48588127..48590527,2	MCF-7	breast:

No data

Variant related genes	Relation type
PFKFB4	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000164045	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1003649	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap]
rs10470687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12107418	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13060933	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13062576	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs13063312	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13070798	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13091944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13094578	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs13100178	0.82[ASN][1000 genomes]
rs13319635	0.98[ASN][1000 genomes]
rs13319651	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13324142	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.83[ASN][1000 genomes]
rs2006871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276850	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276852	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2286652	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2302295	1.00[JPT][hapmap]
rs2310996	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2854394	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2854395	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28563843	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28581474	0.91[ASN][1000 genomes]
rs35064573	0.83[GIH][hapmap]
rs35343040	0.85[ASN][1000 genomes]
rs35562294	0.97[ASN][1000 genomes]
rs35796820	0.83[ASN][1000 genomes]
rs3755819	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	1.00[JPT][hapmap]
rs3821876	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3969942	0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs4075082	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6442126	0.86[CHB][hapmap]
rs6442127	0.81[ASN][1000 genomes]
rs6773261	1.00[JPT][hapmap]
rs6781283	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792156	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs6806059	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs740787	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7428949	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7434077	0.89[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs7434107	0.82[ASN][1000 genomes]
rs7620853	1.00[JPT][hapmap]
rs7623614	0.82[ASN][1000 genomes]
rs7631574	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7640031	0.82[ASN][1000 genomes]
rs7644771	0.82[ASN][1000 genomes]
rs9810549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9810991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9811318	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9812200	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9814951	0.85[GIH][hapmap]
rs9816942	0.82[ASN][1000 genomes]
rs9821797	1.00[JPT][hapmap]
rs9830581	0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9835902	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs9836462	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9837687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9841602	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9843316	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9848824	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9849280	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851743	0.82[ASN][1000 genomes]
rs9851771	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs9864729	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9869698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871180	1.00[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871608	0.82[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9875911	1.00[GIH][hapmap]
rs9878950	0.87[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs9881877	0.93[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9882549	0.83[GIH][hapmap]
rs9882962	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes];0.86[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	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48562600-48592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:48570600-48591600	Weak transcription	Fetal Brain Male	brain
4	chr3:48573600-48592600	Weak transcription	NHDF-Ad	bronchial
5	chr3:48573600-48593400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:48574400-48591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:48574800-48591200	Weak transcription	Dnd41	blood
8	chr3:48576000-48594000	Weak transcription	Small Intestine	intestine
9	chr3:48576400-48591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:48577600-48591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:48578000-48593400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:48581000-48591000	Weak transcription	Lung	lung
13	chr3:48581000-48593600	Weak transcription	Right Atrium	heart
14	chr3:48581200-48593600	Weak transcription	Right Ventricle	heart
15	chr3:48581200-48593800	Weak transcription	Ovary	ovary
16	chr3:48581400-48591600	Weak transcription	Hela-S3	cervix
17	chr3:48581400-48592800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:48582600-48591800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:48583600-48591800	Strong transcription	NHEK	skin
20	chr3:48583800-48591600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:48584200-48593800	Weak transcription	Aorta	Aorta
22	chr3:48584800-48593600	Weak transcription	NH-A	brain
23	chr3:48585000-48591800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:48585000-48593400	Weak transcription	HSMM	muscle
25	chr3:48585200-48592600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:48585200-48593400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:48585200-48593600	Weak transcription	Osteobl	bone
28	chr3:48585400-48592600	Weak transcription	A549	lung
29	chr3:48585800-48591600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:48585800-48593400	Weak transcription	NHLF	lung
31	chr3:48586000-48591600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:48586200-48591000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:48586200-48591200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:48586200-48592600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:48586400-48593200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:48586400-48593400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:48586400-48593400	Enhancers	Pancreas	Pancrea
38	chr3:48586400-48593600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:48586600-48591000	Weak transcription	HMEC	breast
40	chr3:48586600-48592200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:48586600-48592600	Weak transcription	Brain Anterior Caudate	brain
42	chr3:48586600-48592800	Weak transcription	Brain Substantia Nigra	brain
43	chr3:48586600-48593400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:48586600-48593400	Weak transcription	Adipose Nuclei	Adipose
45	chr3:48586600-48593400	Weak transcription	Brain Angular Gyrus	brain
46	chr3:48586600-48593400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:48586800-48592600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:48586800-48592600	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:48586800-48592600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:48586800-48593200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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