Variant report

Variant	rs56090305
Chromosome Location	chr1:151115752-151115753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:151115508-151115850	K562	blood:	n/a	chr1:151115577-151115587
2	CTCF	chr1:151115541-151115811	K562	blood:	n/a	n/a
3	CTCF	chr1:151115629-151115808	K562	blood:	n/a	n/a
4	CTCF	chr1:151115660-151115810	WERI-Rb-1	eye:	n/a	n/a
5	CTCF	chr1:151115620-151115770	WERI-Rb-1	eye:	n/a	n/a
6	CTCF	chr1:151115534-151115846	K562	blood:	n/a	n/a
7	NR2F2	chr1:151115238-151115824	K562	blood:	n/a	n/a
8	ZBTB7A	chr1:151115500-151115798	K562	blood:	n/a	n/a
9	CTCF	chr1:151115697-151115758	K562	blood:	n/a	n/a
10	CTCF	chr1:151115660-151115810	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151112727..151117017-chr1:151118116..151120270,3	K562	blood:
2	chr1:151029687..151031858-chr1:151114009..151116505,2	K562	blood:
3	chr1:151114895..151122057-chr1:151125026..151130825,9	MCF-7	breast:
4	chr1:151115125..151117967-chr1:151253558..151255357,2	K562	blood:
5	chr1:151114839..151116907-chr1:151121689..151124445,2	K562	blood:
6	chr1:151109028..151112291-chr1:151113939..151118222,5	K562	blood:
7	chr1:151114749..151117567-chr1:151151983..151153922,2	K562	blood:
8	chr1:151040013..151045011-chr1:151111761..151118476,6	MCF-7	breast:

No data

Variant related genes	Relation type
SEMA6C	TF binding region
ENSG00000143434	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000213190	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11204782	0.88[ASN][1000 genomes]
rs11807526	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11807847	0.85[ASN][1000 genomes]
rs11810447	0.86[EUR][1000 genomes]
rs11810510	0.90[EUR][1000 genomes]
rs12087892	0.88[ASN][1000 genomes]
rs3811402	0.88[ASN][1000 genomes]
rs56033976	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56299877	0.90[ASN][1000 genomes]
rs7522302	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7523731	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151104400-151116600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:151104400-151117000	Weak transcription	Fetal Kidney	kidney
3	chr1:151104400-151118000	Weak transcription	Aorta	Aorta
4	chr1:151104600-151117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:151104600-151118200	Weak transcription	Primary T cells from cord blood	blood
6	chr1:151105200-151117000	Weak transcription	Placenta	Placenta
7	chr1:151105400-151117000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:151105600-151115800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:151105600-151118000	Weak transcription	Gastric	stomach
10	chr1:151105800-151117200	Weak transcription	Spleen	Spleen
11	chr1:151106200-151116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:151106600-151116000	Strong transcription	Fetal Intestine Small	intestine
13	chr1:151107000-151116600	Weak transcription	HUVEC	blood vessel
14	chr1:151107000-151117600	Weak transcription	Colonic Mucosa	Colon
15	chr1:151107800-151115800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:151108400-151117200	Weak transcription	Brain Substantia Nigra	brain
17	chr1:151108600-151117800	Weak transcription	Esophagus	oesophagus
18	chr1:151109400-151116000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:151109600-151116200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:151109600-151117600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:151110200-151117600	Weak transcription	Pancreas	Pancrea
22	chr1:151110800-151116200	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:151112400-151115800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:151112400-151116200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:151112800-151116600	Weak transcription	Brain Anterior Caudate	brain
26	chr1:151112800-151116600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:151112800-151117400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:151113000-151115800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:151113000-151115800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:151113000-151116000	Weak transcription	Brain Angular Gyrus	brain
31	chr1:151113000-151116400	Weak transcription	Ovary	ovary
32	chr1:151113000-151118000	Weak transcription	Liver	Liver
33	chr1:151114200-151115800	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr1:151114800-151115800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr1:151114800-151115800	Genic enhancers	Fetal Brain Female	brain
36	chr1:151114800-151116200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:151114800-151116200	Genic enhancers	Fetal Muscle Leg	muscle
38	chr1:151114800-151116400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr1:151114800-151116400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:151114800-151116800	Enhancers	Fetal Brain Male	brain
41	chr1:151114800-151116800	Enhancers	Right Atrium	heart
42	chr1:151114800-151117000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr1:151114800-151117200	Enhancers	Left Ventricle	heart
44	chr1:151114800-151117200	Enhancers	Right Ventricle	heart
45	chr1:151114800-151117400	Enhancers	H1 Cell Line	embryonic stem cell
46	chr1:151114800-151117400	Enhancers	Psoas Muscle	Psoas
47	chr1:151114800-151117600	Enhancers	HSMM	muscle
48	chr1:151114800-151117800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:151115000-151116200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:151115000-151118200	Enhancers	K562	blood

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