Variant report

Variant	rs41268727
Chromosome Location	chr1:226254488-226254489
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:226253754-226254595	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:226254102-226254669	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:226254338-226254501	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:226254327-226254579	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:226248810-226256763	K562	blood:	n/a	n/a
6	NFYB	chr1:226254259-226254766	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:226253843-226254736	GM12878	blood:	n/a	n/a
8	NFYB	chr1:226254316-226254746	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:226254221-226254546	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:226253892-226254631	K562	blood:	n/a	n/a
11	POLR2A	chr1:226254257-226254653	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:226252358-226255036	GM12878	blood:	n/a	n/a
13	NFYA	chr1:226254339-226254827	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:226253831-226254551	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:226254270-226254555	MCF-7	breast:	n/a	n/a
16	POLR2A	chr1:226254348-226254625	A549	lung:	n/a	n/a
17	WRNIP1	chr1:226254348-226254562	GM12878	blood:	n/a	n/a
18	RFX5	chr1:226253587-226255011	SK-N-SH	brain:	n/a	chr1:226254507-226254522
19	RFX5	chr1:226254416-226254616	HepG2	liver:	n/a	chr1:226254507-226254522
20	POLR2A	chr1:226254297-226254586	H1-hESC	embryonic stem cell:	n/a	n/a
21	HEY1	chr1:226254188-226254659	K562	blood:	n/a	n/a
22	POLR2A	chr1:226253833-226254698	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:226254383-226254632	GM12891	blood:	n/a	n/a
24	NFYB	chr1:226254340-226254655	K562	blood:	n/a	n/a
25	POLR2A	chr1:226254231-226254586	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:226252953..226257459-chr1:226295699..226299600,6	K562	blood:
2	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:
3	chr1:226252549..226256033-chr1:226258651..226261482,3	MCF-7	breast:
4	chr1:226248537..226252087-chr1:226252328..226257854,13	MCF-7	breast:
5	chr1:226252767..226255693-chr1:226262385..226264510,2	MCF-7	breast:
6	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272562	TF binding region
ENSG00000272562	Chromatin interaction
ENSG00000270598	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000143751	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11583604	1.00[ASN][1000 genomes]
rs11583736	1.00[ASN][1000 genomes]
rs11583805	1.00[ASN][1000 genomes]
rs11585469	1.00[ASN][1000 genomes]
rs11589277	1.00[ASN][1000 genomes]
rs1219670	1.00[ASN][1000 genomes]
rs1219672	1.00[ASN][1000 genomes]
rs1877159	1.00[ASN][1000 genomes]
rs4278344	1.00[ASN][1000 genomes]
rs56170974	1.00[ASN][1000 genomes]
rs72757016	1.00[ASN][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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226252200-226255200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
2	chr1:226252200-226256000	Weak transcription	Lung	lung
3	chr1:226252200-226256400	Weak transcription	Esophagus	oesophagus
4	chr1:226252200-226257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:226252400-226254600	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr1:226252400-226256400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:226252600-226254600	Transcr. at gene 5' and 3'	Hela-S3	cervix
8	chr1:226252600-226255000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:226252800-226254600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:226252800-226254600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
11	chr1:226252800-226255000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:226252800-226257400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:226253000-226254600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:226253000-226254600	Genic enhancers	HSMM	muscle
15	chr1:226253000-226254600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
16	chr1:226253000-226255800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:226253000-226257600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:226253000-226258000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:226253000-226270400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:226253200-226254600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:226253200-226254600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:226253200-226254600	Genic enhancers	Brain Anterior Caudate	brain
23	chr1:226253200-226254600	Genic enhancers	Fetal Muscle Leg	muscle
24	chr1:226253200-226254600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:226253200-226254600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
26	chr1:226253200-226254600	Genic enhancers	A549	lung
27	chr1:226253200-226254600	Genic enhancers	HepG2	liver
28	chr1:226253200-226254800	Genic enhancers	Fetal Stomach	stomach
29	chr1:226253200-226255400	Genic enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:226253200-226255400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:226253200-226256400	Genic enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:226253200-226256600	Genic enhancers	Colon Smooth Muscle	Colon
33	chr1:226253200-226256600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:226253200-226257600	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr1:226253200-226257800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:226253200-226257800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:226253200-226258000	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr1:226253200-226258800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr1:226253200-226260200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr1:226253200-226270400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:226253200-226270600	Weak transcription	Aorta	Aorta
42	chr1:226253400-226254600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr1:226253400-226254600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
44	chr1:226253400-226254600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:226253400-226254600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr1:226253400-226254600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
47	chr1:226253400-226254600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:226253400-226254600	Genic enhancers	Liver	Liver
49	chr1:226253400-226254600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:226253400-226254600	Genic enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links