Variant report

Variant	rs12731039
Chromosome Location	chr1:172535097-172535098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:172534672-172535347	HL-60	blood:	n/a	n/a
2	POLR2A	chr1:172534594-172535162	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:172534378-172535692	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:172535071-172535103	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:172534640-172535954	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:172530178..172532792-chr1:172534437..172536976,3	K562	blood:
2	chr1:172530178..172532826-chr1:172534437..172536976,3	K562	blood:
3	chr1:172527755..172529471-chr1:172533973..172536807,2	K562	blood:
4	chr1:172520454..172524675-chr1:172533729..172536639,3	K562	blood:
5	chr1:172503248..172504952-chr1:172533651..172536311,2	K562	blood:

No data

Variant related genes	Relation type
SUCO	TF binding region
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10489278	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10489279	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12724887	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12727056	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12729335	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12729948	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730136	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12731130	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12737154	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12739997	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12740436	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12743641	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12749864	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12750740	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12752056	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752646	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12753093	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12754650	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12756519	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12758548	1.00[ASW][hapmap];0.83[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12760161	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17370159	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984403	0.87[CEU][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2227189	0.87[ASN][1000 genomes]
rs2516064	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3213552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34134854	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35702642	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35780299	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754424	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68164208	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs730278	0.81[ASN][1000 genomes]
rs7517917	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7549441	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs763109	0.81[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12731039	CD247	cis	parietal	SCAN
rs12731039	SNORD47	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172511800-172557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:172514200-172558800	Weak transcription	Small Intestine	intestine
3	chr1:172516800-172550200	Weak transcription	Fetal Heart	heart
4	chr1:172519200-172559000	Weak transcription	Psoas Muscle	Psoas
5	chr1:172519400-172535400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:172519400-172571600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:172519600-172538000	Weak transcription	Hela-S3	cervix
8	chr1:172519800-172539200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:172521800-172539800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:172521800-172540400	Strong transcription	Primary B cells from cord blood	blood
11	chr1:172521800-172560400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:172523400-172536200	Strong transcription	Primary hematopoietic stem cells	blood
13	chr1:172524000-172538200	Strong transcription	Dnd41	blood
14	chr1:172524000-172538400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:172524000-172540400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr1:172524200-172537400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:172524200-172539600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:172524200-172539600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:172524400-172535200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:172524400-172535800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:172524400-172539000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:172524400-172540000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:172524600-172539800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:172524800-172540400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:172525000-172536000	Strong transcription	Fetal Thymus	thymus
26	chr1:172525000-172540400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:172525200-172537000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr1:172526200-172540400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:172526400-172535400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:172526400-172536000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:172526400-172536200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:172526800-172537000	Weak transcription	Fetal Brain Male	brain
33	chr1:172527000-172539600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:172527000-172558000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr1:172527200-172540000	Weak transcription	Colonic Mucosa	Colon
36	chr1:172527600-172536000	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:172527800-172536800	Weak transcription	HMEC	breast
38	chr1:172527800-172550400	Weak transcription	Stomach Mucosa	stomach
39	chr1:172527800-172554600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:172528000-172537400	Strong transcription	Primary T cells from cord blood	blood
41	chr1:172528400-172535800	Strong transcription	Fetal Stomach	stomach
42	chr1:172528400-172539400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:172528400-172543000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:172528400-172547800	Weak transcription	A549	lung
45	chr1:172528600-172539200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:172528800-172535400	Strong transcription	Left Ventricle	heart
47	chr1:172528800-172537400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:172529000-172538400	Weak transcription	NHDF-Ad	bronchial
49	chr1:172529200-172535600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:172529200-172539800	Weak transcription	NHLF	lung

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