Variant report

Variant	rs2404583
Chromosome Location	chr1:46954554-46954555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46949358..46952077-chr1:46954011..46956367,2	K562	blood:
2	chr1:46942594..46944791-chr1:46952601..46954652,2	K562	blood:
3	chr1:46950640..46959255-chr1:46986389..46991936,15	K562	blood:
4	chr1:46917028..46919676-chr1:46953546..46955125,2	MCF-7	breast:
5	chr1:46945298..46948604-chr1:46953497..46956097,3	K562	blood:
6	chr1:46946915..46950728-chr1:46952343..46956054,5	K562	blood:
7	chr1:46914677..46916878-chr1:46953939..46956178,2	K562	blood:
8	chr1:46953320..46956075-chr1:46979198..46981642,2	MCF-7	breast:
9	chr1:46954039..46957769-chr1:46958689..46962771,8	K562	blood:
10	chr1:46954136..46954641-chr1:46993665..46994197,2	MCF-7	breast:
11	chr1:46954395..46956906-chr1:46986850..46988638,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224863	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11580235	0.83[EUR][1000 genomes]
rs12402727	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12732772	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742745	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756856	0.89[ASN][1000 genomes]
rs12759113	0.90[EUR][1000 genomes]
rs1886116	0.86[EUR][1000 genomes]
rs35827425	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660352	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55644055	0.89[EUR][1000 genomes]
rs942251	0.96[EUR][1000 genomes]
rs998726	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46933200-46955000	Weak transcription	Right Atrium	heart
2	chr1:46951200-46957200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr1:46952600-46954800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:46952800-46955000	Enhancers	K562	blood
5	chr1:46953200-46954600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr1:46953200-46954800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:46953200-46955600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:46953600-46954800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:46953600-46955200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:46953600-46955400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
11	chr1:46953800-46954600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr1:46953800-46956600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr1:46954000-46954600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
14	chr1:46954000-46954800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
15	chr1:46954000-46954800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
16	chr1:46954000-46955000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:46954000-46955600	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr1:46954200-46954600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr1:46954200-46954800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:46954200-46954800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr1:46954200-46955000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr1:46954200-46955000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
23	chr1:46954200-46956200	Bivalent Enhancer	Fetal Intestine Small	intestine
24	chr1:46954400-46954600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:46954400-46954800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:46954400-46954800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:46954400-46955000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr1:46954400-46955200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
29	chr1:46954400-46955200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin

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