Variant report

Variant	rs2474779
Chromosome Location	chr20:25284971-25284972
allele	C/T
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	RUNX3	chr20:25284890-25285209	GM12878	blood:	n/a	n/a
2	POLR2A	chr20:25284701-25285161	A549	lung:	n/a	n/a
3	EBF1	chr20:25284965-25285011	GM12878	blood:	n/a	chr20:25284989-25285000
4	POLR2A	chr20:25284667-25285176	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25274719..25277448-chr20:25283422..25285264,2	K562	blood:

Variant related genes	Relation type
ABHD12	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2474771	1.00[AMR][1000 genomes]
rs2474778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs407925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs496133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs574221	1.00[AFR][1000 genomes]
rs6037118	1.00[AMR][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	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	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
18	nsv912827	chr20:25271326-25288632	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
3	chr20:25249200-25285800	Strong transcription	Dnd41	blood
4	chr20:25249600-25285200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr20:25250800-25285000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:25254400-25287800	Weak transcription	K562	blood
7	chr20:25255800-25290000	Weak transcription	Small Intestine	intestine
8	chr20:25256000-25299400	Weak transcription	Fetal Brain Male	brain
9	chr20:25259000-25290800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr20:25261600-25291000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr20:25266600-25291200	Weak transcription	Primary B cells from cord blood	blood
12	chr20:25267000-25291200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr20:25271400-25290600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr20:25271600-25291200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr20:25273400-25287200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr20:25275400-25285600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr20:25275600-25290400	Strong transcription	Fetal Stomach	stomach
18	chr20:25275800-25285200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr20:25275800-25290600	Strong transcription	Thymus	Thymus
20	chr20:25276200-25285000	Strong transcription	Spleen	Spleen
21	chr20:25276200-25285200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr20:25276200-25285200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr20:25276200-25285200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr20:25276800-25285000	Strong transcription	Primary T cells from cord blood	blood
25	chr20:25277000-25285600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr20:25277600-25285000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr20:25277600-25288000	Strong transcription	Fetal Intestine Small	intestine
28	chr20:25277600-25289200	Weak transcription	Hela-S3	cervix
29	chr20:25277600-25289800	Weak transcription	HSMMtube	muscle
30	chr20:25277600-25291000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr20:25277800-25285800	Strong transcription	Lung	lung
32	chr20:25277800-25286000	Strong transcription	Fetal Intestine Large	intestine
33	chr20:25277800-25290000	Weak transcription	HUVEC	blood vessel
34	chr20:25278000-25287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr20:25278000-25289200	Weak transcription	Stomach Mucosa	stomach
36	chr20:25278200-25287800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr20:25278400-25289600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr20:25278400-25290200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr20:25278600-25285200	Strong transcription	Brain Cingulate Gyrus	brain
40	chr20:25278800-25305600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr20:25279800-25290000	Weak transcription	Colon Smooth Muscle	Colon
42	chr20:25280000-25290600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr20:25280200-25285000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr20:25280400-25285200	Strong transcription	Fetal Brain Female	brain
45	chr20:25280400-25285200	Strong transcription	Gastric	stomach
46	chr20:25280400-25285600	Strong transcription	Placenta	Placenta
47	chr20:25280400-25287600	Weak transcription	Left Ventricle	heart
48	chr20:25280600-25285000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr20:25280600-25285200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr20:25280800-25285000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links