Variant report

Variant	rs73341103
Chromosome Location	chr20:25207484-25207485
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MBD4	chr20:25207423-25208603	HepG2	liver:	n/a	n/a
2	FOSL2	chr20:25207406-25208588	HepG2	liver:	n/a	chr20:25208288-25208299 chr20:25208148-25208160
3	MXI1	chr20:25207407-25208619	SK-N-SH	brain:	n/a	chr20:25207842-25207851 chr20:25207844-25207853
4	MAX	chr20:25207308-25208662	HepG2	liver:	n/a	chr20:25207842-25207853 chr20:25207843-25207852 chr20:25207841-25207854 chr20:25207842-25207853 chr20:25207842-25207852 chr20:25207843-25207852 chr20:25207842-25207853 chr20:25207843-25207852 chr20:25207842-25207852
5	POLR2A	chr20:25207386-25208090	HL-60	blood:	n/a	n/a
6	POLR2A	chr20:25207349-25208233	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr20:25207295-25208607	HepG2	liver:	n/a	n/a
8	MYBL2	chr20:25207433-25208529	HepG2	liver:	n/a	n/a
9	POLR2A	chr20:25207438-25207881	A549	lung:	n/a	n/a
10	POLR2A	chr20:25207436-25208680	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr20:25206151-25207935	A549	lung:	n/a	n/a
12	TCF12	chr20:25207428-25208576	A549	lung:	n/a	n/a
13	TCF12	chr20:25207307-25208364	ECC-1	luminal epithelium:	n/a	chr20:25207419-25207428
14	MAX	chr20:25207388-25208671	A549	lung:	n/a	chr20:25207842-25207853 chr20:25207843-25207852 chr20:25207841-25207854 chr20:25207842-25207853 chr20:25207842-25207852 chr20:25207843-25207852 chr20:25207842-25207853 chr20:25207843-25207852 chr20:25207842-25207852
15	E2F6	chr20:25207307-25208431	A549	lung:	n/a	chr20:25207935-25207942 chr20:25208090-25208107
16	POLR2A	chr20:25207477-25207770	HCT-116	colon:	n/a	n/a
17	POLR2A	chr20:25207397-25208676	K562	blood:	n/a	n/a
18	POLR2A	chr20:25206820-25208593	HepG2	liver:	n/a	n/a
19	JUN	chr20:25207443-25208527	K562	blood:	n/a	chr20:25208048-25208061 chr20:25208288-25208299 chr20:25208148-25208160

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25176141..25177768-chr20:25206257..25208862,2	MCF-7	breast:
2	chr20:25204544..25206460-chr20:25206464..25208599,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268302	TF binding region
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs11907003	1.00[EUR][1000 genomes]
rs11908037	1.00[EUR][1000 genomes]
rs12106059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12106164	1.00[EUR][1000 genomes]
rs12373881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2500428	1.00[EUR][1000 genomes]
rs28435893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28439563	1.00[EUR][1000 genomes]
rs28551104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35022349	1.00[EUR][1000 genomes]
rs35073849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56273742	1.00[EUR][1000 genomes]
rs57218388	1.00[EUR][1000 genomes]
rs57293656	1.00[EUR][1000 genomes]
rs58189090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58410604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58593226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58709664	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58722006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58953621	1.00[AMR][1000 genomes]
rs58957358	1.00[EUR][1000 genomes]
rs59431257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59857017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60459445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60479943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050367	1.00[EUR][1000 genomes]
rs60893899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6106987	1.00[EUR][1000 genomes]
rs7270236	1.00[EUR][1000 genomes]
rs7270324	1.00[AMR][1000 genomes]
rs73331819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331881	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73333142	1.00[EUR][1000 genomes]
rs73333167	1.00[EUR][1000 genomes]
rs73333174	1.00[EUR][1000 genomes]
rs73333187	1.00[EUR][1000 genomes]
rs73333506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73333515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337199	1.00[EUR][1000 genomes]
rs73339096	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341120	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341122	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341124	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341128	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341131	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341135	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341140	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341143	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341155	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341157	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341171	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343043	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343076	1.00[AMR][1000 genomes]
rs73343090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345071	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345087	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345088	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347016	1.00[AMR][1000 genomes]
rs73347023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347066	1.00[AMR][1000 genomes]
rs73348712	1.00[EUR][1000 genomes]
rs73906055	1.00[EUR][1000 genomes]
rs73906057	1.00[EUR][1000 genomes]
rs73906063	1.00[EUR][1000 genomes]
rs73906065	1.00[EUR][1000 genomes]
rs73906067	1.00[EUR][1000 genomes]
rs73906068	1.00[EUR][1000 genomes]
rs73906070	1.00[EUR][1000 genomes]
rs73906071	1.00[EUR][1000 genomes]
rs73906072	1.00[EUR][1000 genomes]
rs8114108	1.00[EUR][1000 genomes]
rs8115188	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8118017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8119273	1.00[EUR][1000 genomes]
rs8120601	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8121557	1.00[EUR][1000 genomes]
rs8123929	1.00[EUR][1000 genomes]
rs8123947	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats 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	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:25190600-25208400	Strong transcription	Thymus	Thymus
4	chr20:25193400-25210800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr20:25196800-25210400	Weak transcription	GM12878-XiMat	blood
6	chr20:25197200-25208000	Weak transcription	Primary B cells from cord blood	blood
7	chr20:25198000-25214000	Weak transcription	Fetal Lung	lung
8	chr20:25198400-25212200	Enhancers	Fetal Heart	heart
9	chr20:25199000-25212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr20:25199200-25208600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:25199200-25210600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr20:25199200-25212000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr20:25199400-25210600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr20:25201600-25208200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr20:25202200-25209600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr20:25202800-25207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr20:25203200-25207600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr20:25204000-25207600	Strong transcription	Spleen	Spleen
19	chr20:25204000-25208200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr20:25204200-25207600	Strong transcription	Brain Cingulate Gyrus	brain
21	chr20:25204200-25208400	Strong transcription	Primary T cells from cord blood	blood
22	chr20:25204200-25208600	Strong transcription	Fetal Intestine Large	intestine
23	chr20:25204200-25213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:25204200-25222800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr20:25204400-25207600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:25204400-25207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr20:25204400-25207800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr20:25204400-25207800	Strong transcription	Dnd41	blood
29	chr20:25204400-25208000	Genic enhancers	A549	lung
30	chr20:25204400-25209200	Strong transcription	Fetal Intestine Small	intestine
31	chr20:25204400-25218200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr20:25204600-25208000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr20:25204800-25207600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr20:25204800-25207600	Weak transcription	HSMM	muscle
35	chr20:25204800-25207800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr20:25204800-25210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr20:25204800-25213600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr20:25205000-25207600	Weak transcription	HUVEC	blood vessel
39	chr20:25205200-25208200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr20:25205400-25207600	Weak transcription	Brain Anterior Caudate	brain
41	chr20:25205400-25207600	Weak transcription	NH-A	brain
42	chr20:25205600-25208600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr20:25206200-25209200	Enhancers	Left Ventricle	heart
44	chr20:25206200-25211400	Enhancers	Right Atrium	heart
45	chr20:25206400-25208600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr20:25206400-25208600	Enhancers	Liver	Liver
47	chr20:25206400-25210000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr20:25206600-25207600	Weak transcription	Brain Angular Gyrus	brain
49	chr20:25206600-25208200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr20:25206600-25208400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links