Variant report

Variant	rs1494533
Chromosome Location	chr15:40510056-40510057
allele	C/T
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	CTCF	chr15:40509188-40510337	SK-N-SH	brain:	n/a	chr15:40509572-40509593
2	CTCF	chr15:40509192-40510118	A549	lung:	n/a	chr15:40509572-40509593
3	POLR2A	chr15:40508883-40510443	K562	blood:	n/a	n/a
4	RAD21	chr15:40509111-40510186	SK-N-SH	brain:	n/a	n/a
5	SMC3	chr15:40509151-40510125	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr15:40510048-40510082	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr15:40509083-40510215	HCT-116	colon:	n/a	chr15:40509572-40509593

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40507899..40511190-chr15:40564977..40567533,3	MCF-7	breast:
2	chr15:40509026..40510811-chr15:40564171..40567983,79	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259288	TF binding region
ENSG00000137843	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11853477	1.00[ASN][1000 genomes]
rs11858747	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494534	0.80[AFR][1000 genomes]
rs1680156	1.00[ASN][1000 genomes]
rs17668261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28750294	0.80[AFR][1000 genomes]
rs35611758	0.81[AFR][1000 genomes]
rs3759843	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs62019997	1.00[ASN][1000 genomes]
rs62020025	1.00[ASN][1000 genomes]
rs62020027	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020029	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020031	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020050	0.96[EUR][1000 genomes]
rs6492939	1.00[CHB][hapmap]
rs7165187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168416	0.81[AFR][1000 genomes]
rs7171605	1.00[ASN][1000 genomes]
rs7173181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178873	0.80[YRI][hapmap]
rs7182070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183293	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389487	0.80[AFR][1000 genomes]
rs74011373	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023415	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40453800-40525000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:40454000-40515200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:40454800-40524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:40455400-40530400	Weak transcription	Fetal Brain Female	brain
5	chr15:40455600-40518200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:40455600-40522200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:40455600-40530400	Weak transcription	Brain Germinal Matrix	brain
8	chr15:40456200-40524000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:40456200-40524000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:40471400-40517600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:40471400-40524400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:40473200-40517800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:40473600-40525200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:40475000-40526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:40475400-40522600	Strong transcription	Dnd41	blood
16	chr15:40481800-40524400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:40483000-40526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:40485400-40513800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:40485400-40527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:40486600-40521000	Weak transcription	Placenta	Placenta
21	chr15:40487600-40518200	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr15:40488200-40517000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr15:40490800-40519000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr15:40491000-40526600	Weak transcription	Primary B cells from cord blood	blood
25	chr15:40491200-40527200	Strong transcription	Fetal Thymus	thymus
26	chr15:40491600-40524600	Weak transcription	Fetal Heart	heart
27	chr15:40491800-40523200	Weak transcription	Esophagus	oesophagus
28	chr15:40492800-40524000	Weak transcription	Fetal Kidney	kidney
29	chr15:40492800-40530800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:40493400-40527000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr15:40496600-40524800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:40497800-40517600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:40498200-40515600	Strong transcription	GM12878-XiMat	blood
34	chr15:40498800-40520600	Weak transcription	NHLF	lung
35	chr15:40502000-40521000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:40503400-40526600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:40504400-40511200	Weak transcription	Fetal Stomach	stomach
38	chr15:40504400-40513600	Weak transcription	Fetal Intestine Small	intestine
39	chr15:40504400-40514000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:40504400-40514200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:40504400-40521600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:40504400-40526400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:40506600-40511800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:40506600-40512200	Weak transcription	Thymus	Thymus
45	chr15:40506800-40524400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:40507000-40510400	Weak transcription	NHEK	skin
47	chr15:40507400-40511200	Weak transcription	Fetal Intestine Large	intestine
48	chr15:40507800-40510400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:40508200-40514200	Strong transcription	Hela-S3	cervix
50	chr15:40508200-40514400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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