Variant report

Variant	rs12731130
Chromosome Location	chr1:172528943-172528944
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:172524779..172527801-chr1:172528773..172532155,3	K562	blood:
2	chr1:172520824..172522644-chr1:172528724..172530286,2	K562	blood:
3	chr1:172527755..172529471-chr1:172533973..172536807,2	K562	blood:
4	chr1:172500697..172503568-chr1:172528002..172531240,3	MCF-7	breast:
5	chr1:172528364..172530709-chr1:172549872..172552272,2	K562	blood:
6	chr1:172417587..172421346-chr1:172527795..172529688,3	MCF-7	breast:
7	chr1:172520150..172522644-chr1:172528070..172530577,3	K562	blood:
8	chr1:172499469..172503029-chr1:172527261..172529453,3	K562	blood:
9	chr1:172500667..172503739-chr1:172526545..172530565,4	K562	blood:
10	chr1:172524779..172527328-chr1:172528773..172530813,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000180999	Chromatin interaction
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10489278	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10489279	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12724887	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727056	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12729335	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729948	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12730136	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12731039	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12737154	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12739997	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12740436	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12743641	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12749864	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12750740	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752056	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12752646	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12753093	0.90[EUR][1000 genomes]
rs12754650	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12756519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758548	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760161	0.87[ASN][1000 genomes]
rs17370159	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227189	0.92[ASN][1000 genomes]
rs2516064	0.93[ASN][1000 genomes]
rs3213552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34134854	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35702642	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35780299	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3754424	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68164208	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs730278	0.85[ASN][1000 genomes]
rs7517917	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7549441	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs763109	0.85[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	nsv872547	chr1:172511969-172545832	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv872548	chr1:172518012-172551724	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172503600-172531600	Weak transcription	Esophagus	oesophagus
2	chr1:172503800-172529000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:172503800-172534200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:172506000-172532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:172509400-172530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:172511800-172557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:172512000-172529000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:172512000-172534200	Weak transcription	Gastric	stomach
9	chr1:172514200-172558800	Weak transcription	Small Intestine	intestine
10	chr1:172514800-172530200	Weak transcription	Thymus	Thymus
11	chr1:172516000-172532800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:172516800-172550200	Weak transcription	Fetal Heart	heart
13	chr1:172518000-172529000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:172518600-172533000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:172519000-172530000	Weak transcription	NH-A	brain
16	chr1:172519000-172530200	Weak transcription	Brain Substantia Nigra	brain
17	chr1:172519200-172529000	Weak transcription	Brain Germinal Matrix	brain
18	chr1:172519200-172534600	Weak transcription	Right Ventricle	heart
19	chr1:172519200-172559000	Weak transcription	Psoas Muscle	Psoas
20	chr1:172519400-172529000	Weak transcription	NHEK	skin
21	chr1:172519400-172533000	Weak transcription	HUVEC	blood vessel
22	chr1:172519400-172534600	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:172519400-172535400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:172519400-172571600	Weak transcription	Brain Angular Gyrus	brain
25	chr1:172519600-172533000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:172519600-172533200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:172519600-172538000	Weak transcription	Hela-S3	cervix
28	chr1:172519800-172534200	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:172519800-172539200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:172521400-172532800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:172521800-172539800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:172521800-172540400	Strong transcription	Primary B cells from cord blood	blood
33	chr1:172521800-172560400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:172523400-172531800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:172523400-172532200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr1:172523400-172536200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr1:172524000-172538200	Strong transcription	Dnd41	blood
38	chr1:172524000-172538400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:172524000-172540400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:172524200-172531400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:172524200-172533000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:172524200-172533000	Weak transcription	Spleen	Spleen
43	chr1:172524200-172537400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:172524200-172539600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:172524200-172539600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:172524400-172533200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:172524400-172535200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:172524400-172535800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:172524400-172539000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:172524400-172540000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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