Variant report

Variant	rs55805005
Chromosome Location	chr2:47216684-47216685
allele	A/G
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	RAD21	chr2:47215972-47216688	HepG2	liver:	n/a	chr2:47216226-47216245
2	EP300	chr2:47215987-47216696	HepG2	liver:	n/a	n/a
3	SMC3	chr2:47211793-47217504	SK-N-SH	brain:	n/a	chr2:47217377-47217391 chr2:47214316-47214330 chr2:47215216-47215224 chr2:47214380-47214394 chr2:47215366-47215376
4	MYBL2	chr2:47215735-47216796	HepG2	liver:	n/a	n/a
5	RAD21	chr2:47212138-47217562	SK-N-SH	brain:	n/a	chr2:47214319-47214328 chr2:47214380-47214394 chr2:47214430-47214443 chr2:47214315-47214334 chr2:47213604-47213614 chr2:47214317-47214324 chr2:47213584-47213596 chr2:47216226-47216245 chr2:47213604-47213616 chr2:47214379-47214398 chr2:47214318-47214331 chr2:47217181-47217195 chr2:47214320-47214332
6	MYBL2	chr2:47216045-47216758	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47213870..47217482-chr2:47217996..47221953,5	MCF-7	breast:
2	chr2:47215935..47217368-chr2:47549916..47551065,3	K562	blood:
3	chr2:47211199..47217347-chr2:47399008..47404700,12	K562	blood:
4	chr2:47144648..47146323-chr2:47215712..47217737,2	MCF-7	breast:
5	chr2:47168191..47171177-chr2:47214556..47217322,3	MCF-7	breast:
6	chr2:47209357..47211157-chr2:47216226..47218870,3	K562	blood:
7	chr2:47209205..47217024-chr2:47399516..47404811,13	MCF-7	breast:
8	chr2:47214614..47216991-chr2:47391312..47393709,3	K562	blood:
9	chr2:47210303..47217706-chr2:47402135..47406405,13	MCF-7	breast:
10	chr2:47212292..47217234-chr2:47401238..47405508,6	K562	blood:

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13399571	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036022	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036033	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17480869	1.00[ASN][1000 genomes]
rs17480988	1.00[ASN][1000 genomes]
rs17481037	1.00[ASN][1000 genomes]
rs17481209	1.00[ASN][1000 genomes]
rs17540157	1.00[ASN][1000 genomes]
rs17540219	1.00[ASN][1000 genomes]
rs17540462	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814035	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55641002	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55824224	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56186415	0.87[ASN][1000 genomes]
rs58637066	1.00[ASN][1000 genomes]
rs58674434	1.00[ASN][1000 genomes]
rs59785154	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60732316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6726941	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6727430	1.00[ASN][1000 genomes]
rs6727529	1.00[ASN][1000 genomes]
rs6751599	1.00[ASN][1000 genomes]
rs6751621	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754795	1.00[ASN][1000 genomes]
rs6755001	1.00[ASN][1000 genomes]
rs72806525	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72806536	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72806537	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72806538	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72806541	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72806558	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806562	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806571	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564728	1.00[ASN][1000 genomes]
rs7576915	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv581750	chr2:47207665-47229953	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47196600-47227800	Strong transcription	Dnd41	blood
2	chr2:47208000-47217400	Enhancers	Stomach Mucosa	stomach
3	chr2:47208600-47219200	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr2:47209400-47217200	Genic enhancers	NHLF	lung
5	chr2:47209600-47217400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:47209600-47218200	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr2:47211400-47217600	Enhancers	Right Atrium	heart
8	chr2:47211800-47218000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:47211800-47218000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:47212000-47217200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:47212000-47217200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:47212000-47217600	Enhancers	Rectal Smooth Muscle	rectum
13	chr2:47212200-47218200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:47212400-47217000	Enhancers	Fetal Heart	heart
15	chr2:47212400-47217600	Enhancers	Fetal Muscle Trunk	muscle
16	chr2:47212600-47217400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:47212800-47217400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:47213000-47217000	Enhancers	Right Ventricle	heart
19	chr2:47213000-47217400	Enhancers	Left Ventricle	heart
20	chr2:47213000-47218000	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:47213000-47221600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:47213400-47217400	Enhancers	Pancreas	Pancrea
23	chr2:47213400-47217600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:47213400-47218000	Enhancers	Brain Angular Gyrus	brain
25	chr2:47213600-47217200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:47213600-47256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:47213800-47216800	Genic enhancers	Fetal Intestine Small	intestine
28	chr2:47213800-47217400	Enhancers	Fetal Brain Male	brain
29	chr2:47213800-47218200	Enhancers	Ovary	ovary
30	chr2:47214000-47262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:47214200-47217200	Enhancers	Fetal Muscle Leg	muscle
32	chr2:47214200-47221000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:47214200-47221200	Weak transcription	Small Intestine	intestine
34	chr2:47214200-47221600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:47214200-47221600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:47214200-47231000	Weak transcription	K562	blood
37	chr2:47214200-47235400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:47214400-47217400	Enhancers	Brain Germinal Matrix	brain
39	chr2:47214400-47217600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:47214600-47217000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:47214600-47217400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr2:47214600-47218400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:47214600-47219200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:47214600-47220000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:47214600-47220600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:47214600-47221200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:47214600-47221600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:47214600-47242000	Strong transcription	Thymus	Thymus
49	chr2:47214800-47217600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:47214800-47219000	Weak transcription	Primary hematopoietic stem cells	blood

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