Variant report

Variant	rs56402847
Chromosome Location	chr1:150127881-150127882
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150125754-150128460	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:150124864-150128792	GM12878	blood:	n/a	n/a
3	MTA3	chr1:150127551-150128164	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:150126108-150128634	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:150127673-150128246	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:150122891-150128842	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:150125817-150129637	GM12891	blood:	n/a	n/a
8	POLR2A	chr1:150127671-150127934	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:150127680-150128234	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:150122674-150136351	U87	brain:	n/a	n/a
11	POLR2A	chr1:150125680-150128604	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:150127224-150128073	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr1:150125993-150128143	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:150126211-150128351	GM12891	blood:	n/a	n/a
15	POLR2A	chr1:150124858-150128702	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:150127577-150128178	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:150126045-150128479	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:150127572-150128151	GM12878	blood:	n/a	n/a
19	NFATC1	chr1:150127457-150128014	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:150125712-150128701	GM12892	blood:	n/a	n/a
21	POLR2A	chr1:150125749-150128270	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:150124720-150136281	U87	brain:	n/a	n/a
23	POLR2A	chr1:150127482-150128755	H1-neurons	neurons:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:149855855..149861458-chr1:150123805..150130441,8	MCF-7	breast:
2	chr1:149856264..149860038-chr1:150127256..150130373,4	MCF-7	breast:
3	chr1:149980635..149983433-chr1:150127638..150130379,2	K562	blood:

No data

Variant related genes	Relation type
PLEKHO1	TF binding region
ENSG00000184260	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000184270	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs55675915	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55730068	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55782319	0.87[AFR][1000 genomes]
rs55917036	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55958060	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56003355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56203821	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56219570	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56235561	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56375233	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56696553	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56775659	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56782368	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56894379	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57259394	1.00[AMR][1000 genomes]
rs57289852	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57459405	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57545744	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57761276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58363747	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58449214	1.00[AMR][1000 genomes]
rs58507490	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58856811	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58978911	0.93[AFR][1000 genomes]
rs59195173	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59354740	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59916811	1.00[AMR][1000 genomes]
rs60442181	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60906570	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61381734	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72694943	0.85[AFR][1000 genomes]
rs7339920	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7339921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7411583	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124293	0.88[AFR][1000 genomes]
rs74124296	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124298	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124299	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124302	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124303	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124304	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124305	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124307	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124312	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124313	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124314	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124315	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124322	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124326	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124329	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124332	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124334	0.98[AFR][1000 genomes]
rs74124337	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124339	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127403	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127404	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127409	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127413	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127422	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127423	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127427	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127429	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127430	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127438	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127439	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127440	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127441	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127443	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127444	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127445	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127446	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127447	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127448	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127449	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127450	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127451	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127452	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127453	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127454	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127455	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127456	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127457	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv535152	chr1:150120726-150143089	Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150123200-150128600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
2	chr1:150123200-150135400	Weak transcription	A549	lung
3	chr1:150123400-150128000	Weak transcription	Gastric	stomach
4	chr1:150123400-150134400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:150123400-150134400	Weak transcription	NHEK	skin
6	chr1:150123800-150131200	Weak transcription	Pancreas	Pancrea
7	chr1:150123800-150134200	Weak transcription	HMEC	breast
8	chr1:150123800-150134600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:150124000-150128000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
10	chr1:150124200-150131000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:150124400-150129000	Weak transcription	Psoas Muscle	Psoas
12	chr1:150124400-150132000	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr1:150124400-150133400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:150124600-150128000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:150124600-150130800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:150124600-150133000	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr1:150124600-150133200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:150124600-150133200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:150124800-150128000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:150124800-150128400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:150124800-150128400	Genic enhancers	Fetal Brain Male	brain
22	chr1:150124800-150132400	Strong transcription	Fetal Intestine Large	intestine
23	chr1:150124800-150133200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:150125000-150128200	Genic enhancers	Fetal Heart	heart
25	chr1:150125000-150132000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:150125200-150131800	Genic enhancers	Primary B cells from cord blood	blood
27	chr1:150125200-150132400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:150125200-150132800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:150125200-150132800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:150125200-150133000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:150125200-150133600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:150125400-150128600	Genic enhancers	Dnd41	blood
33	chr1:150125400-150129600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:150125400-150131200	Strong transcription	HepG2	liver
35	chr1:150125400-150131400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:150125400-150131600	Strong transcription	Fetal Intestine Small	intestine
37	chr1:150125400-150133000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:150125400-150133200	Genic enhancers	HSMM	muscle
39	chr1:150125400-150133600	Genic enhancers	NH-A	brain
40	chr1:150125600-150129400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:150125600-150132200	Genic enhancers	HUVEC	blood vessel
42	chr1:150125600-150132400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr1:150125600-150132400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:150125600-150132800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:150125600-150133200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:150125800-150129200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:150125800-150130200	Strong transcription	Thymus	Thymus
48	chr1:150125800-150130400	Strong transcription	Fetal Lung	lung
49	chr1:150125800-150131000	Genic enhancers	Primary monocytes fromperipheralblood	blood
50	chr1:150125800-150131800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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